Mercurial > repos > nick > dunovo
changeset 11:0f8e0dc73d1d draft default tip
"planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
| author | nick |
|---|---|
| date | Wed, 16 Feb 2022 22:59:00 +0000 |
| parents | 9dc43bf7d1db |
| children | |
| files | align_families.xml correct_barcodes.xml dunovo.xml err.log err2.log make_families.xml out.log out2.log precheck.xml tool_dependencies.xml |
| diffstat | 10 files changed, 5306 insertions(+), 110 deletions(-) [+] |
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--- a/align_families.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/align_families.xml Wed Feb 16 22:59:00 2022 +0000 @@ -1,10 +1,8 @@ <?xml version="1.0"?> -<tool id="align_families" name="Du Novo: Align families" version="2.15"> +<tool id="align_families" name="Du Novo: Align families" version="3.0.2"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="7.221">mafft</requirement> - <requirement type="package" version="2.15">dunovo</requirement> - <!-- TODO: require Python 2.7 --> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <version_command>align-families.py --version</version_command> <command detect_errors="exit_code">align-families.py $check_ids --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' > '$output' @@ -28,6 +26,7 @@ </test> <test> <param name="input" value="families.sort.tsv"/> + <param name="check_ids" value="--no-check-ids"/> <output name="output" file="families.msa.tsv"/> </test> </tests>
--- a/correct_barcodes.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/correct_barcodes.xml Wed Feb 16 22:59:00 2022 +0000 @@ -1,16 +1,17 @@ <?xml version="1.0"?> -<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.15"> +<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="3.0.2"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="1.1.2">bowtie</requirement> - <requirement type="package" version="1.10">networkx</requirement> - <requirement type="package" version="2.15">dunovo</requirement> - <!-- TODO: require Python 2.7 --> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <version_command>correct.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ - baralign.sh -c $advanced.chunkmbs -t \${GALAXY_SLOTS:-1} '$input' refdir correct.sam - && correct.py --galaxy $phone $check_ids --dist $dist --mapq $mapq --pos $pos + baralign.sh -c $advanced.chunkmbs -t \${GALAXY_SLOTS:-1} -g + #if $phone == '--phone-home': + -p + #end if + '$input' refdir correct.sam + && correct.py --galaxy $phone $check_ids $allow_no_nm_if_ns --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa correct.sam > families.corrected.tsv && sort families.corrected.tsv @@ -19,11 +20,12 @@ </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> - <param name="dist" type="integer" value="3" min="1" label="Maximum differences" help="Only use alignments where the barcodes differ by at most these many errors. Note that raising this beyond 3 probably won't have an effect, because of the inherent limit in bowtie's ability to match up distant barcodes."/> + <param name="dist" type="integer" value="3" min="1" label="Maximum differences" help="Only use alignments where the barcodes differ by at most these many errors. Note that raising this beyond 3 won't have an effect, because of the inherent limit in bowtie's ability to match up distant barcodes."/> <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/> <param name="pos" type="integer" value="2" min="0" label="Maximum start offset" help="Ignore alignments where the start positions differ by more than this."/> <param name="check_ids" type="boolean" truevalue="" falsevalue="--no-check-ids" checked="True" label="Check read names" help="Make sure reads are properly paired up. The job will fail if there is a pair of reads where their ids aren't identical (minus any ending /1 or /2)."/> - <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET"/> + <param name="allow_no_nm_if_ns" type="boolean" truevalue="--allow-no-nm-if-ns" falsevalue="" checked="False" label="Allow missing NM tags" help="Allow alignments with missing NM tags if the barcode has at least one N. Try checking this if you get the error "Alignment missing NM tag, but likely due to N's in sequence"."/> + <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time and memory taken to process it, some performance-related parameters, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET"/> <section name="advanced" title="Advanced Options" expanded="false"> <param name="chunkmbs" type="integer" value="512" min="16" label="bowtie --chunkmbs" help="This is the number of megabytes to give each bowtie thread for storing path descriptors. If you see warnings about "Exhausted best-first chunk memory" in stderr, you need to increase this."/> </section>
--- a/dunovo.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/dunovo.xml Wed Feb 16 22:59:00 2022 +0000 @@ -1,9 +1,8 @@ <?xml version="1.0"?> -<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.15"> +<tool id="dunovo" name="Du Novo: Make consensus reads" version="3.0.2"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="2.15">dunovo</requirement> - <!-- TODO: require Python 2.7 --> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <version_command>make-consensi.py --version</version_command> <command detect_errors="exit_code"> @@ -11,16 +10,21 @@ #if $out_format.type == 'fastq': --fastq-out $out_format.qual #end if - --qual $qual_thres --qual-format $qual_format --min-reads $min_reads --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' + --aligner $advanced.aligner --qual $qual_thres --qual-format $qual_format --min-reads $min_reads --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' #if $keep_sscs: --sscs1 '$sscs1' --sscs2 '$sscs2' #end if </command> <inputs> <param name="input" type="data" format="tabular" label="Aligned input reads" /> - <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads for a consensus" help="This many reads are necessary to form a single-strand consensus sequence. Families smaller than this will be skipped."/> - <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="Consensus % threshold" help="The consensus base must be present in more than this fraction of the reads, or "N" will be used instead."/> - <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="The consensus base must be present in more than this absolute number of reads, or "N" will be used instead."/> + <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads for a consensus" help="This many reads are necessary to form a single-strand consensus sequence. Families smaller than this will be skipped and no consensus (single or duplex) will be produced."/> + <param name="cons_thres" type="float" value="0.7" min="0" max="1.0" label="Consensus % threshold" help="Each consensus base must be present in more than this fraction of the reads, or "N" will be used instead."/> + <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="Each consensus base must be present in more than this absolute number of reads, or "N" will be used instead. The "Consensus % threshold" sets a threshold based on the number of reads in the family, while this threshold is a fixed, absolute number. If both are used, the consensus base must pass both requirements."/> + <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> + <param name="qual_format" type="select" label="Input quality score format" help="Format of the FASTQ files of the raw reads. Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> + <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> + <option value="solexa">Solexa (PHRED 0 = "@")</option> + </param> <conditional name="out_format"> <param name="type" type="select" label="Output format"> <option value="fasta" selected="true">FASTA</option> @@ -30,13 +34,14 @@ <param name="qual" type="integer" value="40" min="0" max="93" label="Output PHRED score" help="There is currently no way to output a meaningful quality score for consensus bases. You'll have to specify an artificial one, which will be given to every base. A good value is 40, the maximum score normally output by sequencers. This means the bases won't be inadvertently filtered out by some downstream tool."/> </when> </conditional> - <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> - <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> - <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> - <option value="solexa">Solexa (PHRED 0 = "@")</option> - </param> <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the number of processes used, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/> + <section name="advanced" title="Advanced Options" expanded="false"> + <param name="aligner" type="select" value="biopython" label="Pairwise sequence aligner" help="Which pairwise alignment library to use. "BioPython" uses BioPython's PairwiseAligner and a substitution matrix built by Bioconductor's Biostrings package. "swalign" is a custom Smith-Waterman implementation by Nicolaus Lance Hepler. It is deprecated and kept only for backward compatibility."> + <option value="biopython">BioPython</option> + <option value="swalign">swalign</option> + </param> + </section> </inputs> <outputs> <data name="dcs1" label="$tool.name on $on_string (mate 1)">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/err.log Wed Feb 16 22:59:00 2022 +0000 @@ -0,0 +1,728 @@ +planemo couldn't find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data. +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +Cloning into '/tmp/tmppmuqm8bo/galaxy-dev'... +done. +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.0" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^3.4.2" +warning Resolution field "ua-parser-js@0.7.30" is incompatible with requested version "ua-parser-js@0.7.22" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.4" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8" +warning "@galaxyproject/bootstrap-tour > bootstrap@5.0.2" has unmet peer dependency "@popperjs/core@^2.9.2". +warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0". +warning " > @hirez_io/observer-spy@2.0.0" has unmet peer dependency "typescript@>=2.8.1". +warning " > linkifyjs@2.1.9" has unmet peer dependency "react@>= 0.14.0". +warning " > linkifyjs@2.1.9" has unmet peer dependency "react-dom@>= 0.14.0". +warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. 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Upgrade to chokidar 3 with 15x fewer dependencies +warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0". +warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported +warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning axios@0.19.2: Critical security vulnerability fixed in v0.21.1. For more information, see https://github.com/axios/axios/pull/3410 +warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported +warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning package.json: License should be a valid SPDX license expression +warning openseadragon@2.4.2: License should be a valid SPDX license expression +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning package.json: License should be a valid SPDX license expression +warning bio-pv > sniper > ecstatic@0.5.8: This package is unmaintained and deprecated. See the GH Issue 259. +warning bio-pv > sniper > swig@1.4.2: This package is no longer maintained +warning bio-pv > sniper > biojs-util-snippets > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning bio-pv > browserify > glob > minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue +warning bio-pv > browserify > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning bio-pv > sniper > biojs-util-snippets > request > har-validator@5.1.5: this library is no longer supported +warning bio-pv > sniper > biojs-util-snippets > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > babylon-walk > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning fbjs > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +Browserslist: caniuse-lite is outdated. Please run: +npx browserslist@latest --update-db +Browserslist: caniuse-lite is outdated. Please run: +npx browserslist@latest --update-db +[BABEL] Note: The code generator has deoptimised the styling of /tmp/tmppmuqm8bo/galaxy-dev/client/node_modules/bootstrap-vue/esm/icons/icons.js as it exceeds the max of 500KB. +duplicate attribute: :writable +[BABEL] Note: The code generator has deoptimised the styling of /tmp/tmppmuqm8bo/galaxy-dev/client/node_modules/handsontable/dist/handsontable.js as it exceeds the max of 500KB. +Browserslist: caniuse-lite is outdated. Please run next command `yarn upgrade caniuse-lite browserslist` +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +[2022-02-16 16:20:15 -0500] [2610616] [INFO] Starting gunicorn 20.1.0 +[2022-02-16 16:20:15 -0500] [2610616] [INFO] Listening at: http://127.0.0.1:9090 (2610616) +[2022-02-16 16:20:15 -0500] [2610616] [INFO] Using worker: sync +[2022-02-16 16:20:15 -0500] [2610618] [INFO] Booting worker with pid: 2610618 +DEBUG:galaxy.app:python path is: /tmp/tmppmuqm8bo/galaxy-dev/lib, /tmp/tmppmuqm8bo/galaxy-dev, /home/me/.planemo/gx_venv_3/bin, /usr/lib/python38.zip, /usr/lib/python3.8, /usr/lib/python3.8/lib-dynload, /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages +DEBUG:galaxy.config:Configuration directory is /tmp/tmppmuqm8bo +DEBUG:galaxy.config:Data directory is /tmp/tmppmuqm8bo/galaxy-dev/database +DEBUG:galaxy.config:Managed config directory is /tmp/tmppmuqm8bo +DEBUG:galaxy.containers:config file '/tmp/tmppmuqm8bo/containers_conf.yml' does not exist, running with default config +galaxy.model.migrate.check INFO 2022-02-16 16:20:19,706 [pN:MainProcess,p:2610618,tN:MainThread] Creating database for URI [sqlite:////tmp/tmppmuqm8bo/galaxy.sqlite?isolation_level=IMMEDIATE] +galaxy.model.migrate.check INFO 2022-02-16 16:20:19,707 [pN:MainProcess,p:2610618,tN:MainThread] Creating new database from scratch, skipping migrations +galaxy.config INFO 2022-02-16 16:20:21,165 [pN:MainProcess,p:2610618,tN:MainThread] Install database targetting Galaxy's database configuration. +galaxy.web_stack.handlers INFO 2022-02-16 16:20:21,198 [pN:main,p:2610618,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default +galaxy.jobs INFO 2022-02-16 16:20:21,198 [pN:main,p:2610618,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2022-02-16 16:20:21,198 [pN:main,p:2610618,tN:MainThread] Tag [_default_] handlers: main +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py:587: SAWarning: relationship 'RepositoryRepositoryDependencyAssociation.repository' will copy column tool_shed_repository.id to column repository_repository_dependency_association.tool_shed_repository_id, which conflicts with relationship(s): 'ToolShedRepository.required_repositories' (copies tool_shed_repository.id to repository_repository_dependency_association.tool_shed_repository_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="required_repositories"' to the 'RepositoryRepositoryDependencyAssociation.repository' relationship. + for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \ +galaxy.queue_worker INFO 2022-02-16 16:20:21,557 [pN:main,p:2610618,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmppmuqm8bo/galaxy.sqlite?isolation_level=IMMEDIATE +galaxy.tools.data INFO 2022-02-16 16:20:21,574 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/all_fasta.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,574 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/bfast_indexes.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,575 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/blastdb.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,575 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/blastdb_p.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,575 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/blastdb_d.loc, reading sample +galaxy.tools.data WARNING 2022-02-16 16:20:21,576 [pN:main,p:2610618,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tools.data WARNING 2022-02-16 16:20:21,576 [pN:main,p:2610618,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tools.data INFO 2022-02-16 16:20:21,576 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/maf_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,577 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,577 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/perm_base_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/perm_color_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/picard_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/picard_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/mosaik_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,579 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/twobit.loc, reading sample +galaxy.tools.data WARNING 2022-02-16 16:20:21,687 [pN:main,p:2610618,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): +<Server-Side Genome List> +galaxy.tools.data INFO 2022-02-16 16:20:21,688 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/liftOver.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,689 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/bam_iobio.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,689 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/vcf_iobio.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,690 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/biom_simple_display.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,690 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/intermine_simple_display.loc, reading sample +galaxy.tools.data INFO 2022-02-16 16:20:21,691 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/icn3d_simple_display.loc, reading sample +galaxy.util WARNING 2022-02-16 16:20:21,838 [pN:main,p:2610618,tN:MainThread] directory not found: /tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2022-02-16 16:20:21,838 [pN:main,p:2610618,tN:MainThread] The default shed tool config file (/tmp/tmppmuqm8bo/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2022-02-16 16:20:21,838 [pN:main,p:2610618,tN:MainThread] Parsing the tool configuration /tmp/tmppmuqm8bo/tool_conf.xml +galaxy.tools WARNING 2022-02-16 16:20:21,855 [pN:main,p:2610618,tN:MainThread] Tool with id 'dunovo': a when tag has not been defined for 'out_format (type) --> fasta', assuming empty inputs. +galaxy.util ERROR 2022-02-16 16:20:21,856 [pN:main,p:2610618,tN:MainThread] Error parsing file /home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml +Traceback (most recent call last): + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/__init__.py", line 255, in parse_xml + tree = etree.parse(fname, parser=parser) + File "src/lxml/etree.pyx", line 3521, in lxml.etree.parse + File "src/lxml/parser.pxi", line 1859, in lxml.etree._parseDocument + File "src/lxml/parser.pxi", line 1885, in lxml.etree._parseDocumentFromURL + File "src/lxml/parser.pxi", line 1789, in lxml.etree._parseDocFromFile + File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile + File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc + File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult + File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError + File "/home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml", line 27 +lxml.etree.XMLSyntaxError: Attribute label redefined, line 27, column 336 +galaxy.tool_util.toolbox.base ERROR 2022-02-16 16:20:21,857 [pN:main,p:2610618,tN:MainThread] Failed to load potential tool /home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml. +Traceback (most recent call last): + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 902, in quick_load + tool = self.load_tool(tool_file, tool_cache_data_dir) + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 942, in load_tool + tool = self.create_tool(config_file=config_file, tool_shed_repository=tool_shed_repository, guid=guid, tool_cache_data_dir=tool_cache_data_dir, **kwds) + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tools/__init__.py", line 374, in create_tool + tool_source = self.get_expanded_tool_source(config_file) + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tools/__init__.py", line 391, in get_expanded_tool_source + raise e + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tools/__init__.py", line 382, in get_expanded_tool_source + return get_tool_source( + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_util/parser/factory.py", line 44, in get_tool_source + tree, macro_paths = load_tool_with_refereces(config_file) + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/xml_macros.py", line 15, in load_with_references + tree = raw_xml_tree(path) + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/xml_macros.py", line 56, in raw_xml_tree + tree = parse_xml(path, strip_whitespace=False, remove_comments=True) + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/__init__.py", line 255, in parse_xml + tree = etree.parse(fname, parser=parser) + File "src/lxml/etree.pyx", line 3521, in lxml.etree.parse + File "src/lxml/parser.pxi", line 1859, in lxml.etree._parseDocument + File "src/lxml/parser.pxi", line 1885, in lxml.etree._parseDocumentFromURL + File "src/lxml/parser.pxi", line 1789, in lxml.etree._parseDocFromFile + File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile + File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc + File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult + File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError + File "/home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml", line 27 +lxml.etree.XMLSyntaxError: Attribute label redefined, line 27, column 336 +galaxy.tools WARNING 2022-02-16 16:20:21,862 [pN:main,p:2610618,tN:MainThread] The default shed tool config file (/tmp/tmppmuqm8bo/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2022-02-16 16:20:21,863 [pN:main,p:2610618,tN:MainThread] Parsing the tool configuration /tmp/tmppmuqm8bo/shed_tools_conf.xml +galaxy.tools WARNING 2022-02-16 16:20:21,863 [pN:main,p:2610618,tN:MainThread] The default shed tool config file (/tmp/tmppmuqm8bo/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2022-02-16 16:20:21,863 [pN:main,p:2610618,tN:MainThread] Parsing the tool configuration /tmp/tmppmuqm8bo/empty_tool_conf.xml +galaxy.datatypes.display_applications.application ERROR 2022-02-16 16:20:21,979 [pN:main,p:2610618,tN:MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. +galaxy.datatypes.display_applications.application ERROR 2022-02-16 16:20:21,981 [pN:main,p:2610618,tN:MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,280 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,282 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,283 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,283 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,284 [pN:main,p:2610618,tN:MainThread] Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,285 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,285 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,286 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,287 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,287 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,288 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,289 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,289 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,293 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,296 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,296 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,296 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,297 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,297 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,301 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,304 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,306 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,308 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,310 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,311 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,311 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,313 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,315 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,316 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,320 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,322 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,323 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,325 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,329 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,333 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,337 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,341 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,344 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,348 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,353 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,357 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,362 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,363 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,367 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,369 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,370 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,371 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,373 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,373 [pN:main,p:2610618,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping... +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,374 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,374 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,374 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,375 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2022-02-16 16:20:22,413 [pN:main,p:2610618,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.tours._impl INFO 2022-02-16 16:20:22,427 [pN:main,p:2610618,tN:MainThread] Loaded tour 'core.scratchbook' +galaxy.tours._impl INFO 2022-02-16 16:20:22,446 [pN:main,p:2610618,tN:MainThread] Loaded tour 'core.history' +galaxy.jobs INFO 2022-02-16 16:20:22,455 [pN:main,p:2610618,tN:MainThread] Handler 'main' will load all configured runner plugins +galaxy.jobs.handler INFO 2022-02-16 16:20:22,463 [pN:main,p:2610618,tN:MainThread] job handler stop queue started +galaxy.jobs.handler INFO 2022-02-16 16:20:22,479 [pN:main,p:2610618,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): _default_ +galaxy.jobs.handler INFO 2022-02-16 16:20:22,479 [pN:main,p:2610618,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2022-02-16 16:20:22,481 [pN:main,p:2610618,tN:MainThread] job handler stop queue started +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:359: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(hda_not_ready), +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(ldda_not_ready)) +galaxy.workflow.scheduling_manager INFO 2022-02-16 16:20:22,506 [pN:main,p:2610618,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler. +galaxy.web_stack.handlers INFO 2022-02-16 16:20:22,506 [pN:main,p:2610618,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default +galaxy.jobs.handler INFO 2022-02-16 16:20:22,507 [pN:main,p:2610618,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): None, _default_ +galaxy.queue_worker INFO 2022-02-16 16:20:22,510 [pN:main,p:2610618,tN:MainThread] Binding and starting galaxy control worker for main +galaxy.queue_worker INFO 2022-02-16 16:20:22,526 [pN:main,p:2610618,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main. +galaxy.app INFO 2022-02-16 16:20:22,673 [pN:main,p:2610618,tN:MainThread] Galaxy app startup finished (3269.979 ms) +galaxy.queue_worker INFO 2022-02-16 16:20:22,718 [pN:main,p:2610618,tN:Thread-1] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:359: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(hda_not_ready), +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(ldda_not_ready)) +galaxy.web_stack INFO 2022-02-16 16:20:24,422 [pN:main,p:2610618,tN:MainThread] Galaxy server instance 'main' is running +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/webapps/base/webapp.py:607: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + user = self.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == remote_user_email).first() +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/webapps/base/webapp.py:243: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + if config.use_remote_user and self.galaxy_session.user.deleted: +127.0.0.1 - - [16/Feb/2022:16:20:24 -0400] "HEAD / HTTP/1.1" 200 - "-" "curl/7.68.0" +127.0.0.1 - - [16/Feb/2022:16:21:25 -0400] "GET / HTTP/1.1" 200 - "http://localhost:9090/admin/toolbox_dependencies" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/__init__.py:2669: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + rval = db_session.query( +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /welcome HTTP/1.1" 302 265 "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/tools?in_panel=true&view=default HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/histories/2891970512fa2d5a/contents?limit=500&offset=0&details=54f2a3a23292eb07%2Ca90a30fafe298e1e%2Cb54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:27 -0400] "GET /history/set_as_current?id=2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:16:21:27 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/managers/histories.py:570: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + for hda in history.datasets: +127.0.0.1 - - [16/Feb/2022:16:21:27 -0400] "GET /api/histories/2891970512fa2d5a?view=betawebclient HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +[2022-02-16 16:21:34 -0500] [2610616] [INFO] Handling signal: int +[2022-02-16 16:21:34 -0500] [2610618] [INFO] Worker exiting (pid: 2610618) +galaxy.jobs.handler ERROR 2022-02-16 16:21:34,396 [pN:main,p:2610618,tN:JobHandlerQueue.monitor_thread] Exception in monitor_step +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: job + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 307, in __monitor + self.__monitor_step() + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 325, in __monitor_step + self.__handle_waiting_jobs() + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 373, in __handle_waiting_jobs + jobs_to_check = ready_query.all() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all + return self._iter().all() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job +[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id +FROM history_dataset_collection_association, job_to_output_dataset_collection +WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id +FROM history_dataset_association, job_to_output_dataset +WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 +FROM job LEFT OUTER JOIN galaxy_user ON galaxy_user.id = job.user_id +WHERE job.state = ? AND job.handler = ? AND (job.id NOT IN (SELECT anon_3.id +FROM (SELECT job.id AS id +FROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id +WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_3)) AND (job.id NOT IN (SELECT anon_4.id +FROM (SELECT job.id AS id +FROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id +WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_4)) ORDER BY job.id] +[parameters: (<states.NEW: 'new'>, 'main', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata')] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +kombu.mixins WARNING 2022-02-16 16:21:34,671 [pN:main,p:2610618,tN:Thread-1] Connection to broker lost, trying to re-establish connection... +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: kombu_queue + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 172, in run + for _ in self.consume(limit=None, **kwargs): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 194, in consume + conn.drain_events(timeout=safety_interval) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/connection.py", line 318, in drain_events + return self.transport.drain_events(self.connection, **kwargs) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 960, in drain_events + get(self._deliver, timeout=timeout) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get + return self.fun(resource, callback, **kwargs) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 998, in _drain_channel + return channel.drain_events(callback=callback, timeout=timeout) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 742, in drain_events + return self._poll(self.cycle, callback, timeout=timeout) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 399, in _poll + return cycle.get(callback) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get + return self.fun(resource, callback, **kwargs) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 402, in _get_and_deliver + message = self._get(queue) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 112, in _get + obj = self._get_or_create(queue) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 79, in _get_or_create + obj = self.session.query(self.queue_cls) \ + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first + return self.limit(1)._iter().first() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: kombu_queue +[SQL: SELECT kombu_queue.id AS kombu_queue_id, kombu_queue.name AS kombu_queue_name +FROM kombu_queue +WHERE kombu_queue.name = ? + LIMIT ? OFFSET ?] +[parameters: ('control.main@aziz', 1, 0)] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +galaxy.app ERROR 2022-02-16 16:21:34,675 [pN:main,p:2610618,tN:MainThread] Failed to shutdown database heartbeat cleanly +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: worker_process + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first + return self.limit(1)._iter().first() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process +[SQL: SELECT worker_process.id AS worker_process_id, worker_process.server_name AS worker_process_server_name, worker_process.hostname AS worker_process_hostname, worker_process.pid AS worker_process_pid, worker_process.update_time AS worker_process_update_time +FROM worker_process +WHERE worker_process.server_name = ? AND worker_process.hostname = ? + LIMIT ? OFFSET ?] +[parameters: ('main', 'aziz', 1, 0)] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +galaxy.jobs.handler INFO 2022-02-16 16:21:34,676 [pN:main,p:2610618,tN:MainThread] sending stop signal to worker thread +galaxy.jobs.handler ERROR 2022-02-16 16:21:35,057 [pN:main,p:2610618,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: job + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all + return self._iter().all() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job +[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id +FROM history_dataset_collection_association, job_to_output_dataset_collection +WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id +FROM history_dataset_association, job_to_output_dataset +WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 +FROM job +WHERE job.state IN (?, ?, ?) AND job.handler = ?] +[parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +galaxy.jobs.handler INFO 2022-02-16 16:21:35,676 [pN:main,p:2610618,tN:MainThread] job handler queue stopped +galaxy.jobs.runners INFO 2022-02-16 16:21:35,676 [pN:main,p:2610618,tN:MainThread] LocalRunner: Sending stop signal to 4 job worker threads +galaxy.jobs.runners INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] Waiting up to 30 seconds for job worker threads to shutdown... +galaxy.jobs.runners INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] All job worker threads shutdown cleanly +galaxy.jobs.handler INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] sending stop signal to worker thread +galaxy.jobs.handler INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] job handler stop queue stopped +Error in atexit._run_exitfuncs: +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: worker_process + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown + File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first + return self.limit(1)._iter().first() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process +[SQL: SELECT worker_process.id AS worker_process_id, worker_process.server_name AS worker_process_server_name, worker_process.hostname AS worker_process_hostname, worker_process.pid AS worker_process_pid, worker_process.update_time AS worker_process_update_time +FROM worker_process +WHERE worker_process.server_name = ? AND worker_process.hostname = ? + LIMIT ? OFFSET ?] +[parameters: ('main', 'aziz', 1, 0)] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 16:21:35,859 [pN:main,p:2610618,tN:MainThread] Exception during reset or similar +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy + fairy._reset(pool) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset + pool._dialect.do_rollback(self) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback + dbapi_connection.rollback() +sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140222822082304 and this is thread id 140224748214080. +sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 16:21:35,860 [pN:main,p:2610618,tN:MainThread] Exception closing connection <sqlite3.Connection object at 0x7f88065f34e0> +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy + fairy._reset(pool) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset + pool._dialect.do_rollback(self) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback + dbapi_connection.rollback() +sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140222822082304 and this is thread id 140224748214080. + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 244, in _close_connection + self._dialect.do_close(connection) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 673, in do_close + dbapi_connection.close() +sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140222822082304 and this is thread id 140224748214080. +[2022-02-16 16:21:36 -0500] [2610616] [INFO] Shutting down: Master +Traceback (most recent call last): + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 665, in _config_directory + yield config_directory + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config + yield LocalGalaxyConfig( + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config + yield config + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 48, in _serve + exit_code = run_galaxy_command( + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/run.py", line 118, in run_galaxy_command + exit_code = shell(command, env=env) + File "/home/me/.local/lib/python3.8/site-packages/galaxy/util/commands.py", line 60, in shell + return p.wait() + File "/usr/lib/python3.8/subprocess.py", line 1083, in wait + return self._wait(timeout=timeout) + File "/usr/lib/python3.8/subprocess.py", line 1806, in _wait + (pid, sts) = self._try_wait(0) + File "/usr/lib/python3.8/subprocess.py", line 1764, in _try_wait + (pid, sts) = os.waitpid(self.pid, wait_flags) +KeyboardInterrupt + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/home/me/.local/bin/planemo", line 8, in <module> + sys.exit(planemo()) + File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__ + return self.main(*args, **kwargs) + File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main + rv = self.invoke(ctx) + File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke + return _process_result(sub_ctx.command.invoke(sub_ctx)) + File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke + return ctx.invoke(self.callback, **ctx.params) + File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke + return callback(*args, **kwargs) + File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func + return ctx.invoke(f, obj, *args, **kwargs) + File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke + return callback(*args, **kwargs) + File "/home/me/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options + return f(*args, **kwds) + File "/home/me/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli + galaxy_serve(ctx, runnables, **kwds) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve + return _serve(ctx, runnables, **kwds) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 72, in _serve + return config + File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__ + self.gen.throw(type, value, traceback) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config + yield config + File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__ + self.gen.throw(type, value, traceback) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config + yield LocalGalaxyConfig( + File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__ + self.gen.throw(type, value, traceback) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 669, in _config_directory + shutil.rmtree(config_directory) + File "/usr/lib/python3.8/shutil.py", line 722, in rmtree + onerror(os.rmdir, path, sys.exc_info()) + File "/usr/lib/python3.8/shutil.py", line 720, in rmtree + os.rmdir(path) +OSError: [Errno 39] Directory not empty: '/tmp/tmppmuqm8bo'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/err2.log Wed Feb 16 22:59:00 2022 +0000 @@ -0,0 +1,1139 @@ +planemo couldn't find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data. +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +Cloning into '/tmp/tmp1upz926i/galaxy-dev'... +done. +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.0" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^3.4.2" +warning Resolution field "ua-parser-js@0.7.30" is incompatible with requested version "ua-parser-js@0.7.22" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.4" +warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8" +warning "@galaxyproject/bootstrap-tour > bootstrap@5.0.2" has unmet peer dependency "@popperjs/core@^2.9.2". +warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0". +warning " > @hirez_io/observer-spy@2.0.0" has unmet peer dependency "typescript@>=2.8.1". +warning " > linkifyjs@2.1.9" has unmet peer dependency "react@>= 0.14.0". +warning " > linkifyjs@2.1.9" has unmet peer dependency "react-dom@>= 0.14.0". +warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported +warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning Workspaces can only be enabled in private projects. +warning plotly.js > color-rgba > color-space > mumath@3.3.4: Redundant dependency in your project. +warning copy-webpack-plugin > webpack-log > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin +warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0". +warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported +warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning fbjs > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning hyphy-vision > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1 +warning hyphy-vision > alignment.js > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1 +warning hyphy-vision > extract-text-webpack-plugin@2.1.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin +warning hyphy-vision > alignment.js > phylotree > rollup-plugin-node-resolve@3.4.0: This package has been deprecated and is no longer maintained. Please use @rollup/plugin-node-resolve. +warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning "hyphy-vision > extract-text-webpack-plugin@2.1.2" has incorrect peer dependency "webpack@^2.2.0". +warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin +warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0". +warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported +warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning axios@0.19.2: Critical security vulnerability fixed in v0.21.1. For more information, see https://github.com/axios/axios/pull/3410 +warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported +warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning package.json: License should be a valid SPDX license expression +warning openseadragon@2.4.2: License should be a valid SPDX license expression +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning package.json: License should be a valid SPDX license expression +warning bio-pv > browserify > glob > minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue +warning bio-pv > browserify > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning bio-pv > sniper > ecstatic@0.5.8: This package is unmaintained and deprecated. See the GH Issue 259. +warning bio-pv > sniper > swig@1.4.2: This package is no longer maintained +warning bio-pv > sniper > biojs-util-snippets > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning bio-pv > sniper > biojs-util-snippets > request > har-validator@5.1.5: this library is no longer supported +warning bio-pv > sniper > biojs-util-snippets > request > uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details. +warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning parcel-bundler > babylon-walk > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x. +warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142 +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +warning fbjs > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies +warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. +warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. +warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated +warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated +Browserslist: caniuse-lite is outdated. Please run: +npx browserslist@latest --update-db +Browserslist: caniuse-lite is outdated. Please run: +npx browserslist@latest --update-db +[BABEL] Note: The code generator has deoptimised the styling of /tmp/tmp1upz926i/galaxy-dev/client/node_modules/bootstrap-vue/esm/icons/icons.js as it exceeds the max of 500KB. +duplicate attribute: :writable +[BABEL] Note: The code generator has deoptimised the styling of /tmp/tmp1upz926i/galaxy-dev/client/node_modules/handsontable/dist/handsontable.js as it exceeds the max of 500KB. +Browserslist: caniuse-lite is outdated. Please run next command `yarn upgrade caniuse-lite browserslist` +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +[2022-02-16 17:19:24 -0500] [2654000] [INFO] Starting gunicorn 20.1.0 +[2022-02-16 17:19:24 -0500] [2654000] [INFO] Listening at: http://127.0.0.1:9090 (2654000) +[2022-02-16 17:19:24 -0500] [2654000] [INFO] Using worker: sync +[2022-02-16 17:19:24 -0500] [2654005] [INFO] Booting worker with pid: 2654005 +DEBUG:galaxy.app:python path is: /tmp/tmp1upz926i/galaxy-dev/lib, /tmp/tmp1upz926i/galaxy-dev, /home/me/.planemo/gx_venv_3/bin, /usr/lib/python38.zip, /usr/lib/python3.8, /usr/lib/python3.8/lib-dynload, /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages +DEBUG:galaxy.config:Configuration directory is /tmp/tmp1upz926i +DEBUG:galaxy.config:Data directory is /tmp/tmp1upz926i/galaxy-dev/database +DEBUG:galaxy.config:Managed config directory is /tmp/tmp1upz926i +DEBUG:galaxy.containers:config file '/tmp/tmp1upz926i/containers_conf.yml' does not exist, running with default config +galaxy.model.migrate.check INFO 2022-02-16 17:19:28,513 [pN:MainProcess,p:2654005,tN:MainThread] Creating database for URI [sqlite:////tmp/tmp1upz926i/galaxy.sqlite?isolation_level=IMMEDIATE] +galaxy.model.migrate.check INFO 2022-02-16 17:19:28,514 [pN:MainProcess,p:2654005,tN:MainThread] Creating new database from scratch, skipping migrations +galaxy.config INFO 2022-02-16 17:19:29,872 [pN:MainProcess,p:2654005,tN:MainThread] Install database targetting Galaxy's database configuration. +galaxy.web_stack.handlers INFO 2022-02-16 17:19:29,895 [pN:main,p:2654005,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default +galaxy.jobs INFO 2022-02-16 17:19:29,895 [pN:main,p:2654005,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2022-02-16 17:19:29,895 [pN:main,p:2654005,tN:MainThread] Tag [_default_] handlers: main +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py:587: SAWarning: relationship 'RepositoryRepositoryDependencyAssociation.repository' will copy column tool_shed_repository.id to column repository_repository_dependency_association.tool_shed_repository_id, which conflicts with relationship(s): 'ToolShedRepository.required_repositories' (copies tool_shed_repository.id to repository_repository_dependency_association.tool_shed_repository_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="required_repositories"' to the 'RepositoryRepositoryDependencyAssociation.repository' relationship. + for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \ +galaxy.queue_worker INFO 2022-02-16 17:19:30,292 [pN:main,p:2654005,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmp1upz926i/galaxy.sqlite?isolation_level=IMMEDIATE +galaxy.tools.data INFO 2022-02-16 17:19:30,309 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/all_fasta.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,309 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/bfast_indexes.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,310 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/blastdb.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,310 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/blastdb_p.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/blastdb_d.loc, reading sample +galaxy.tools.data WARNING 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tools.data WARNING 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tools.data INFO 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/maf_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,312 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,312 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/perm_base_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/perm_color_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/picard_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/picard_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/mosaik_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,314 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/twobit.loc, reading sample +galaxy.tools.data WARNING 2022-02-16 17:19:30,403 [pN:main,p:2654005,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): +<Server-Side Genome List> +galaxy.tools.data INFO 2022-02-16 17:19:30,404 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/liftOver.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,405 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/bam_iobio.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,406 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/vcf_iobio.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,406 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/biom_simple_display.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,407 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/intermine_simple_display.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,407 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/icn3d_simple_display.loc, reading sample +galaxy.util WARNING 2022-02-16 17:19:30,585 [pN:main,p:2654005,tN:MainThread] directory not found: /tmp/tmp1upz926i/galaxy-dev/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2022-02-16 17:19:30,586 [pN:main,p:2654005,tN:MainThread] The default shed tool config file (/tmp/tmp1upz926i/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2022-02-16 17:19:30,586 [pN:main,p:2654005,tN:MainThread] Parsing the tool configuration /tmp/tmp1upz926i/tool_conf.xml +galaxy.tools WARNING 2022-02-16 17:19:30,608 [pN:main,p:2654005,tN:MainThread] Tool with id 'dunovo': a when tag has not been defined for 'out_format (type) --> fasta', assuming empty inputs. +galaxy.tools WARNING 2022-02-16 17:19:30,619 [pN:main,p:2654005,tN:MainThread] The default shed tool config file (/tmp/tmp1upz926i/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2022-02-16 17:19:30,619 [pN:main,p:2654005,tN:MainThread] Parsing the tool configuration /tmp/tmp1upz926i/shed_tools_conf.xml +galaxy.tools WARNING 2022-02-16 17:19:30,619 [pN:main,p:2654005,tN:MainThread] The default shed tool config file (/tmp/tmp1upz926i/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2022-02-16 17:19:30,619 [pN:main,p:2654005,tN:MainThread] Parsing the tool configuration /tmp/tmp1upz926i/empty_tool_conf.xml +galaxy.datatypes.display_applications.application ERROR 2022-02-16 17:19:30,724 [pN:main,p:2654005,tN:MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. +galaxy.datatypes.display_applications.application ERROR 2022-02-16 17:19:30,726 [pN:main,p:2654005,tN:MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:30,997 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,997 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,002 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,003 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,006 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,007 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,009 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,010 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,014 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,015 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,017 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,018 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,020 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,021 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,023 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,025 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,026 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,028 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,029 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,030 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,032 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,035 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,038 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,039 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,040 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,043 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,044 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,045 [pN:main,p:2654005,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping... +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,045 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,046 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,046 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,047 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2022-02-16 17:19:31,068 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.tours._impl INFO 2022-02-16 17:19:31,074 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.scratchbook' +galaxy.tours._impl INFO 2022-02-16 17:19:31,093 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.history' +galaxy.jobs INFO 2022-02-16 17:19:31,108 [pN:main,p:2654005,tN:MainThread] Handler 'main' will load all configured runner plugins +galaxy.jobs.handler INFO 2022-02-16 17:19:31,120 [pN:main,p:2654005,tN:MainThread] job handler stop queue started +galaxy.jobs.handler INFO 2022-02-16 17:19:31,137 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): _default_ +galaxy.jobs.handler INFO 2022-02-16 17:19:31,137 [pN:main,p:2654005,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2022-02-16 17:19:31,139 [pN:main,p:2654005,tN:MainThread] job handler stop queue started +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py:359: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(hda_not_ready), +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(ldda_not_ready)) +galaxy.workflow.scheduling_manager INFO 2022-02-16 17:19:31,192 [pN:main,p:2654005,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler. +galaxy.web_stack.handlers INFO 2022-02-16 17:19:31,197 [pN:main,p:2654005,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default +galaxy.jobs.handler INFO 2022-02-16 17:19:31,199 [pN:main,p:2654005,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): None, _default_ +galaxy.queue_worker INFO 2022-02-16 17:19:31,202 [pN:main,p:2654005,tN:MainThread] Binding and starting galaxy control worker for main +galaxy.queue_worker INFO 2022-02-16 17:19:31,216 [pN:main,p:2654005,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main. +galaxy.app INFO 2022-02-16 17:19:31,373 [pN:main,p:2654005,tN:MainThread] Galaxy app startup finished (3111.728 ms) +galaxy.queue_worker INFO 2022-02-16 17:19:31,411 [pN:main,p:2654005,tN:Thread-1] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py:359: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(hda_not_ready), +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + ~model.Job.table.c.id.in_(ldda_not_ready)) +galaxy.web_stack INFO 2022-02-16 17:19:33,106 [pN:main,p:2654005,tN:MainThread] Galaxy server instance 'main' is running +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/webapps/base/webapp.py:607: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + user = self.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == remote_user_email).first() +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/webapps/base/webapp.py:243: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + if config.use_remote_user and self.galaxy_session.user.deleted: +127.0.0.1 - - [16/Feb/2022:17:19:33 -0400] "HEAD / HTTP/1.1" 200 - "-" "curl/7.68.0" +127.0.0.1 - - [16/Feb/2022:17:24:00 -0400] "GET / HTTP/1.1" 200 - "http://localhost:9090/datasets/b842d972534ccb3e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/__init__.py:2669: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + rval = db_session.query( +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /welcome HTTP/1.1" 302 265 "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/tools?in_panel=true&view=default HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/histories/2891970512fa2d5a/contents?limit=500&offset=0&details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /history/set_as_current?id=2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/managers/histories.py:525: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + 'empty': lambda i, k, **c: (len(i.datasets) + len(i.dataset_collections)) <= 0, +127.0.0.1 - - [16/Feb/2022:17:24:01 -0400] "GET /api/histories/2891970512fa2d5a?view=betawebclient HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:11 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:11 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:11 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:11 -0400] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:11 -0400] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:22 -0400] "POST /api/uploads HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:22,679 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (34.599 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:22,820 [pN:main,p:2654005,tN:MainThread] (Job[id=1,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:22 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:22 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A01.681Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:22 -0400] "POST /api/uploads HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:22,987 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (21.183 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:23,084 [pN:main,p:2654005,tN:MainThread] (Job[id=2,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:22 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:23 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A22.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/__init__.py:1440: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + .where(HistoryDatasetCollectionAssociation.table.c.id.in_(subq)) \ +galaxy.jobs.handler INFO 2022-02-16 17:24:23,572 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.handler INFO 2022-02-16 17:24:23,740 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:23,827 [pN:main,p:2654005,tN:LocalRunner.work_thread-0] Built script [/tmp/tmp1upz926i/job_working_directory/000/1/tool_script.sh] for tool command [python '/tmp/tmp1upz926i/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp1upz926i/galaxy-dev' '/tmp/tmp1upz926i/job_working_directory/000/1/registry.xml' '/tmp/tmp1upz926i/job_working_directory/000/1/upload_params.json' '1:/tmp/tmp1upz926i/job_working_directory/000/1/working/dataset_1_files:/tmp/tmp1upz926i/files/000/dataset_1.dat'] +galaxy.jobs.command_factory INFO 2022-02-16 17:24:23,958 [pN:main,p:2654005,tN:LocalRunner.work_thread-1] Built script [/tmp/tmp1upz926i/job_working_directory/000/2/tool_script.sh] for tool command [python '/tmp/tmp1upz926i/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp1upz926i/galaxy-dev' '/tmp/tmp1upz926i/job_working_directory/000/2/registry.xml' '/tmp/tmp1upz926i/job_working_directory/000/2/upload_params.json' '2:/tmp/tmp1upz926i/job_working_directory/000/2/working/dataset_2_files:/tmp/tmp1upz926i/files/000/dataset_2.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:27 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A23.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:30 -0400] "GET /api/tools/precheck/build?version=3.0.2&__identifer=40d6p2ywjn5&tool_version=3.0.2 HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:30 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:30 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:30 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:30 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:30 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:30 -0400] "GET /api/tools/precheck/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A27.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:33 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:35,395 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (24.284 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,416 [pN:main,p:2654005,tN:MainThread] Handled output named output1 for tool CONVERTER_gz_to_uncompressed (0.957 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,416 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (0.175 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,418 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=CONVERTER_gz_to_uncompressed] complete, ready to be enqueued (0.967 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,437 [pN:main,p:2654005,tN:MainThread] Flushed transaction for job Job[id=3,tool_id=CONVERTER_gz_to_uncompressed] (19.325 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:35,449 [pN:main,p:2654005,tN:MainThread] Flushed transaction for Job[id=3,tool_id=CONVERTER_gz_to_uncompressed] (11.057 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:35,449 [pN:main,p:2654005,tN:MainThread] (Job[id=3,tool_id=CONVERTER_gz_to_uncompressed]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +galaxy.tools.actions INFO 2022-02-16 17:24:35,529 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool precheck (0.824 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,538 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (8.923 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,540 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=precheck] complete, ready to be enqueued (1.379 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:35,558 [pN:main,p:2654005,tN:MainThread] (Job[id=4,tool_id=precheck]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:35 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:35 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A31.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:35 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:35 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:35 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:24:36,218 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:36,321 [pN:main,p:2654005,tN:LocalRunner.work_thread-2] Built script [/tmp/tmp1upz926i/job_working_directory/000/3/tool_script.sh] for tool command [cp '/tmp/tmp1upz926i/job_working_directory/000/3/configs/tmp4ea73yop' 'galaxy.json' && gzip -dcf '/tmp/tmp1upz926i/files/000/dataset_1.dat' > '/tmp/tmp1upz926i/files/000/dataset_3.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:39 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A35.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:39 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:24:40,402 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:40,536 [pN:main,p:2654005,tN:LocalRunner.work_thread-3] Built script [/tmp/tmp1upz926i/job_working_directory/000/4/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; precheck.py --no-check-ids --tag-length 12 --constant-length 5 --min-reads 3 '/tmp/tmp1upz926i/files/000/dataset_3.dat' '/tmp/tmp1upz926i/files/000/dataset_2.dat' > '/tmp/tmp1upz926i/files/000/dataset_4.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:43 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A39.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:43 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:43 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:44 -0400] "GET /api/tools/make_families/build?version=3.0.2&__identifer=zn5n7gxymri&tool_version=3.0.2 HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:44 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:44 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:44 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:44 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:44 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:44 -0400] "GET /api/tools/make_families/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:47 -0400] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:47 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A43.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:47 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:47 -0400] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:47 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:48 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:48 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:48 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/8155e4b4bf1581ff HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:50,841 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (25.627 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:50,864 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool make_families (0.943 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:50,885 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (21.017 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:50,886 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=make_families] complete, ready to be enqueued (1.339 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:50,908 [pN:main,p:2654005,tN:MainThread] (Job[id=5,tool_id=make_families]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:50 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:50 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A47.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:50 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:51 -0400] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:51 -0400] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:24:51,907 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:52,048 [pN:main,p:2654005,tN:LocalRunner.work_thread-0] Built script [/tmp/tmp1upz926i/job_working_directory/000/5/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; make-consensi.py --version > /tmp/tmp1upz926i/job_working_directory/000/5/outputs/COMMAND_VERSION 2>&1; make-families.sh -t 12 -i 5 '/tmp/tmp1upz926i/files/000/dataset_3.dat' '/tmp/tmp1upz926i/files/000/dataset_2.dat' > '/tmp/tmp1upz926i/files/000/dataset_5.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /api/tools/correct_barcodes/build?version=3.0.2&__identifer=zqs52bkurng&tool_version=3.0.2 HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /api/tools/correct_barcodes/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:55 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A50.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:55 -0400] "POST /api/tools/correct_barcodes/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:59 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A55.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:59 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:59 -0400] "POST /api/tools/correct_barcodes/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:59 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:59 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:59 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:25:01,164 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (11.425 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:01,197 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool correct_barcodes (1.188 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:01,213 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (16.650 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:01,215 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=correct_barcodes] complete, ready to be enqueued (1.661 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:25:01,250 [pN:main,p:2654005,tN:MainThread] (Job[id=6,tool_id=correct_barcodes]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:25:01 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:01 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A59.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:01 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:01 -0400] "POST /api/tools/correct_barcodes/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:25:02,399 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:25:02,522 [pN:main,p:2654005,tN:LocalRunner.work_thread-1] Built script [/tmp/tmp1upz926i/job_working_directory/000/6/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; correct.py --version > /tmp/tmp1upz926i/job_working_directory/000/6/outputs/COMMAND_VERSION 2>&1; baralign.sh -c 512 -t ${GALAXY_SLOTS:-1} -g '/tmp/tmp1upz926i/files/000/dataset_5.dat' refdir correct.sam && correct.py --galaxy --no-check-ids --dist 3 --mapq 20 --pos 2 '/tmp/tmp1upz926i/files/000/dataset_5.dat' refdir/barcodes.fa correct.sam > families.corrected.tsv && sort families.corrected.tsv > '/tmp/tmp1upz926i/files/000/dataset_6.dat'] +127.0.0.1 - - [16/Feb/2022:17:25:03 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/7b55dbb89df8f4e5 HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:05 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A01.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:05 -0400] "POST /api/tools/correct_barcodes/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:08 -0400] "GET /api/tools/align_families/build?version=3.0.2&__identifer=vace8ey3usq&tool_version=3.0.2 HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:08 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:08 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:08 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:08 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:08 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:08 -0400] "GET /api/tools/align_families/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:09 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A05.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:09 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:09 -0400] "POST /api/tools/align_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:09 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:09 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:09 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:25:22,658 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (10.704 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:22,676 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool align_families (0.967 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:22,685 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (8.847 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:22,687 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=align_families] complete, ready to be enqueued (1.427 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:25:22,707 [pN:main,p:2654005,tN:MainThread] (Job[id=7,tool_id=align_families]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:25:22 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:22 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A09.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:22 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:22 -0400] "POST /api/tools/align_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:25:23,244 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:25:23,341 [pN:main,p:2654005,tN:LocalRunner.work_thread-2] Built script [/tmp/tmp1upz926i/job_working_directory/000/7/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; align-families.py --version > /tmp/tmp1upz926i/job_working_directory/000/7/outputs/COMMAND_VERSION 2>&1; align-families.py --no-check-ids --aligner kalign --galaxy --processes ${GALAXY_SLOTS:-1} '/tmp/tmp1upz926i/files/000/dataset_6.dat' > '/tmp/tmp1upz926i/files/000/dataset_7.dat'] +127.0.0.1 - - [16/Feb/2022:17:25:26 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A22.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:26 -0400] "POST /api/tools/align_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:28 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/fa6d20d0fb68383f HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:29 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/683bc220e21425bb?keys=rerunnable%2Ccreating_job HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:30 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e%2C683bc220e21425bb&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A26.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:31 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:31 -0400] "POST /api/tools/align_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:31 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:31 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:31 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:32 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/683bc220e21425bb HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:35 -0400] "GET /api/tools/make_families/build?version=3.0.2&__identifer=xwrkqkk592&tool_version=3.0.2 HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:35 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:35 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:35 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:35 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:35 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:35 -0400] "GET /api/tools/make_families/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:36 -0400] "GET /api/tools/dunovo/build?version=3.0.2&__identifer=7uf3g9o8xek&tool_version=3.0.2 HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:36 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:37 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:37 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:37 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:37 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:37 -0400] "GET /api/tools/dunovo/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:25:50,497 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (16.036 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,523 [pN:main,p:2654005,tN:MainThread] Handled output named dcs1 for tool dunovo (3.862 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,525 [pN:main,p:2654005,tN:MainThread] Handled output named dcs2 for tool dunovo (2.181 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,535 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (9.707 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,537 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=dunovo] complete, ready to be enqueued (1.539 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:25:50,560 [pN:main,p:2654005,tN:MainThread] (Job[id=8,tool_id=dunovo]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:25:50 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:50 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A30.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:50 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:50 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:25:51,414 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.security.object_wrapper WARNING 2022-02-16 17:25:51,498 [pN:main,p:2654005,tN:LocalRunner.work_thread-3] Unable to create dynamic subclass SafeStringWrapper(galaxy.model.none_like.None:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.security.object_wrapper.SafeStringWrapper'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'numbers.Number'>) for <class 'galaxy.model.none_like.NoneDataset'>, None: type() doesn't support MRO entry resolution; use types.new_class() +galaxy.jobs.command_factory INFO 2022-02-16 17:25:51,526 [pN:main,p:2654005,tN:LocalRunner.work_thread-3] Built script [/tmp/tmp1upz926i/job_working_directory/000/8/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; make-consensi.py --version > /tmp/tmp1upz926i/job_working_directory/000/8/outputs/COMMAND_VERSION 2>&1; make-consensi.py --galaxy --processes ${GALAXY_SLOTS:-1} --aligner biopython --qual 25 --qual-format sanger --min-reads 3 --cons-thres 0.5 --min-cons-reads 0 '/tmp/tmp1upz926i/files/000/dataset_7.dat' --dcs1 '/tmp/tmp1upz926i/files/000/dataset_8.dat' --dcs2 '/tmp/tmp1upz926i/files/000/dataset_9.dat'] +127.0.0.1 - - [16/Feb/2022:17:25:54 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A50.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:54 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:55 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:58 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A54.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:00 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:02 -0400] "GET /api/jobs/a90a30fafe298e1e/build_for_rerun HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:02 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:02 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:02 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:02 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:02 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:02 -0400] "GET /api/tools/dunovo/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:06 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:26:15,534 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (18.785 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,555 [pN:main,p:2654005,tN:MainThread] Handled output named dcs1 for tool dunovo (1.139 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,556 [pN:main,p:2654005,tN:MainThread] Handled output named dcs2 for tool dunovo (0.677 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,558 [pN:main,p:2654005,tN:MainThread] Handled output named sscs1 for tool dunovo (2.141 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,560 [pN:main,p:2654005,tN:MainThread] Handled output named sscs2 for tool dunovo (1.773 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,570 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (10.279 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,572 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=dunovo] complete, ready to be enqueued (1.936 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:26:15,593 [pN:main,p:2654005,tN:MainThread] (Job[id=9,tool_id=dunovo]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:26:15 -0400] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:15 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A59.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:15 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:15 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:26:16,479 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:26:16,612 [pN:main,p:2654005,tN:LocalRunner.work_thread-0] Built script [/tmp/tmp1upz926i/job_working_directory/000/9/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; make-consensi.py --version > /tmp/tmp1upz926i/job_working_directory/000/9/outputs/COMMAND_VERSION 2>&1; make-consensi.py --galaxy --processes ${GALAXY_SLOTS:-1} --fastq-out 40 --aligner swalign --qual 25 --qual-format sanger --min-reads 3 --cons-thres 0.5 --min-cons-reads 0 '/tmp/tmp1upz926i/files/000/dataset_7.dat' --dcs1 '/tmp/tmp1upz926i/files/000/dataset_10.dat' --dcs2 '/tmp/tmp1upz926i/files/000/dataset_11.dat' --sscs1 '/tmp/tmp1upz926i/files/000/dataset_12.dat' --sscs2 '/tmp/tmp1upz926i/files/000/dataset_13.dat'] +127.0.0.1 - - [16/Feb/2022:17:26:18 -0400] "GET /api/jobs/b842d972534ccb3e/build_for_rerun HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:18 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:18 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:19 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:19 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:19 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:19 -0400] "GET /api/tools/dunovo/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:19 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A26%3A15.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:20 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:20 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:20 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:20 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:21 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/__init__.py:383: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. + return self.text_metrics + self.numeric_metrics +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/jobs/b842d972534ccb3e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/jobs/b842d972534ccb3e?full=true HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/metrics?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/jobs/b842d972534ccb3e/destination_params HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/configuration/decode/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/configuration/decode/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/683bc220e21425bb HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/9ce08b2254e4d5ed HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:23 -0400] "GET /api/datasets/80b8022ff3f677b7 HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:23 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A26%3A19.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:28 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/jobs/b842d972534ccb3e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/datasets/b54fb481e575bccc/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration/decode/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/datasets/b54fb481e575bccc/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/datasets/b54fb481e575bccc/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration/decode/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:00 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/5449172d6ff5669b HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:22 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/80b8022ff3f677b7 HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:24 -0400] "GET /datasets/80b8022ff3f677b7/display/?preview=True HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/jobs/b842d972534ccb3e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration/decode/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/metrics?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration/decode/80b8022ff3f677b7 HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:35 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:37 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/jobs/a90a30fafe298e1e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/jobs/a90a30fafe298e1e?full=true HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/metrics?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/jobs/a90a30fafe298e1e/destination_params HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/configuration/decode/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/configuration/decode/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +[2022-02-16 17:28:33 -0500] [2654000] [INFO] Handling signal: int +[2022-02-16 17:28:33 -0500] [2654005] [INFO] Worker exiting (pid: 2654005) +galaxy.jobs.handler ERROR 2022-02-16 17:28:34,121 [pN:main,p:2654005,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: job + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor + self.monitor_step() + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step + newly_deleted_jobs = self.sa_session.query(model.Job).enable_eagerloads(False) \ + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all + return self._iter().all() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job +[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id +FROM history_dataset_collection_association, job_to_output_dataset_collection +WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id +FROM history_dataset_association, job_to_output_dataset +WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 +FROM job +WHERE job.state IN (?, ?, ?) AND job.handler = ?] +[parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +galaxy.jobs.handler ERROR 2022-02-16 17:28:34,777 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] Exception in monitor_step +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: job + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 307, in __monitor + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 325, in __monitor_step + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 373, in __handle_waiting_jobs + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all + return self._iter().all() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job +[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id +FROM history_dataset_collection_association, job_to_output_dataset_collection +WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id +FROM history_dataset_association, job_to_output_dataset +WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 +FROM job LEFT OUTER JOIN galaxy_user ON galaxy_user.id = job.user_id +WHERE job.state = ? AND job.handler = ? AND (job.id NOT IN (SELECT anon_3.id +FROM (SELECT job.id AS id +FROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id +WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_3)) AND (job.id NOT IN (SELECT anon_4.id +FROM (SELECT job.id AS id +FROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id +WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_4)) ORDER BY job.id] +[parameters: (<states.NEW: 'new'>, 'main', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata')] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +kombu.mixins WARNING 2022-02-16 17:28:34,851 [pN:main,p:2654005,tN:Thread-1] Connection to broker lost, trying to re-establish connection... +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: kombu_queue + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 172, in run + for _ in self.consume(limit=None, **kwargs): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 194, in consume + conn.drain_events(timeout=safety_interval) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/connection.py", line 318, in drain_events + return self.transport.drain_events(self.connection, **kwargs) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 960, in drain_events + get(self._deliver, timeout=timeout) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get + return self.fun(resource, callback, **kwargs) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 998, in _drain_channel + return channel.drain_events(callback=callback, timeout=timeout) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 742, in drain_events + return self._poll(self.cycle, callback, timeout=timeout) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 399, in _poll + return cycle.get(callback) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get + return self.fun(resource, callback, **kwargs) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 402, in _get_and_deliver + message = self._get(queue) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 112, in _get + obj = self._get_or_create(queue) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 79, in _get_or_create + obj = self.session.query(self.queue_cls) \ + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first + return self.limit(1)._iter().first() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: kombu_queue +[SQL: SELECT kombu_queue.id AS kombu_queue_id, kombu_queue.name AS kombu_queue_name +FROM kombu_queue +WHERE kombu_queue.name = ? + LIMIT ? OFFSET ?] +[parameters: ('control.main@aziz', 1, 0)] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +galaxy.app ERROR 2022-02-16 17:28:34,855 [pN:main,p:2654005,tN:MainThread] Failed to shutdown database heartbeat cleanly +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: worker_process + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first + return self.limit(1)._iter().first() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process +[SQL: SELECT worker_process.id AS worker_process_id, worker_process.server_name AS worker_process_server_name, worker_process.hostname AS worker_process_hostname, worker_process.pid AS worker_process_pid, worker_process.update_time AS worker_process_update_time +FROM worker_process +WHERE worker_process.server_name = ? AND worker_process.hostname = ? + LIMIT ? OFFSET ?] +[parameters: ('main', 'aziz', 1, 0)] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +galaxy.jobs.handler INFO 2022-02-16 17:28:34,855 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread +galaxy.jobs.handler ERROR 2022-02-16 17:28:35,130 [pN:main,p:2654005,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: job + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all + return self._iter().all() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job +[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id +FROM history_dataset_collection_association, job_to_output_dataset_collection +WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id +FROM history_dataset_association, job_to_output_dataset +WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 +FROM job +WHERE job.state IN (?, ?, ?) AND job.handler = ?] +[parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +galaxy.jobs.handler INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] job handler queue stopped +galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] LocalRunner: Sending stop signal to 4 job worker threads +galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] Waiting up to 30 seconds for job worker threads to shutdown... +galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] All job worker threads shutdown cleanly +galaxy.jobs.handler INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread +galaxy.jobs.handler INFO 2022-02-16 17:28:35,857 [pN:main,p:2654005,tN:MainThread] job handler stop queue stopped +Error in atexit._run_exitfuncs: +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlite3.OperationalError: no such table: worker_process + +The above exception was the direct cause of the following exception: + +Traceback (most recent call last): + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first + return self.limit(1)._iter().first() + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter + result = self.session.execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute + result = conn._execute_20(statement, params or {}, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20 + return meth(self, args_10style, kwargs_10style, execution_options) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection + return connection._execute_clauseelement( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement + ret = self._execute_context( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context + self._handle_dbapi_exception( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception + util.raise_( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ + raise exception + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context + self.dialect.do_execute( + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute + cursor.execute(statement, parameters) +sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process +[SQL: SELECT worker_process.id AS worker_process_id, worker_process.server_name AS worker_process_server_name, worker_process.hostname AS worker_process_hostname, worker_process.pid AS worker_process_pid, worker_process.update_time AS worker_process_update_time +FROM worker_process +WHERE worker_process.server_name = ? AND worker_process.hostname = ? + LIMIT ? OFFSET ?] +[parameters: ('main', 'aziz', 1, 0)] +(Background on this error at: http://sqlalche.me/e/14/e3q8) +sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 17:28:36,070 [pN:main,p:2654005,tN:MainThread] Exception during reset or similar +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy + fairy._reset(pool) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset + pool._dialect.do_rollback(self) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback + dbapi_connection.rollback() +sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140196716734208 and this is thread id 140198646921024. +sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 17:28:36,071 [pN:main,p:2654005,tN:MainThread] Exception closing connection <sqlite3.Connection object at 0x7f82368a03f0> +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy + fairy._reset(pool) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset + pool._dialect.do_rollback(self) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback + dbapi_connection.rollback() +sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140196716734208 and this is thread id 140198646921024. + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 244, in _close_connection + self._dialect.do_close(connection) + File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 673, in do_close + dbapi_connection.close() +sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140196716734208 and this is thread id 140198646921024. +[2022-02-16 17:28:36 -0500] [2654000] [INFO] Shutting down: Master +Traceback (most recent call last): + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 665, in _config_directory + yield config_directory + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config + yield LocalGalaxyConfig( + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config + yield config + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 48, in _serve + exit_code = run_galaxy_command( + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/run.py", line 118, in run_galaxy_command + exit_code = shell(command, env=env) + File "/home/me/.local/lib/python3.8/site-packages/galaxy/util/commands.py", line 60, in shell + return p.wait() + File "/usr/lib/python3.8/subprocess.py", line 1083, in wait + return self._wait(timeout=timeout) + File "/usr/lib/python3.8/subprocess.py", line 1806, in _wait + (pid, sts) = self._try_wait(0) + File "/usr/lib/python3.8/subprocess.py", line 1764, in _try_wait + (pid, sts) = os.waitpid(self.pid, wait_flags) +KeyboardInterrupt + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/home/me/.local/bin/planemo", line 8, in <module> + sys.exit(planemo()) + File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__ + return self.main(*args, **kwargs) + File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main + rv = self.invoke(ctx) + File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke + return _process_result(sub_ctx.command.invoke(sub_ctx)) + File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke + return ctx.invoke(self.callback, **ctx.params) + File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke + return callback(*args, **kwargs) + File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func + return ctx.invoke(f, obj, *args, **kwargs) + File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke + return callback(*args, **kwargs) + File "/home/me/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options + return f(*args, **kwds) + File "/home/me/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli + galaxy_serve(ctx, runnables, **kwds) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve + return _serve(ctx, runnables, **kwds) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 72, in _serve + return config + File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__ + self.gen.throw(type, value, traceback) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config + yield config + File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__ + self.gen.throw(type, value, traceback) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config + yield LocalGalaxyConfig( + File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__ + self.gen.throw(type, value, traceback) + File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 669, in _config_directory + shutil.rmtree(config_directory) + File "/usr/lib/python3.8/shutil.py", line 722, in rmtree + onerror(os.rmdir, path, sys.exc_info()) + File "/usr/lib/python3.8/shutil.py", line 720, in rmtree + os.rmdir(path) +OSError: [Errno 39] Directory not empty: '/tmp/tmp1upz926i'
--- a/make_families.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/make_families.xml Wed Feb 16 22:59:00 2022 +0000 @@ -1,10 +1,9 @@ <?xml version="1.0"?> -<tool id="make_families" name="Du Novo: Make families" version="2.15"> +<tool id="make_families" name="Du Novo: Make families" version="3.0.2"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="2.15">dunovo</requirement> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> - <!-- TODO: Add dependency on coreutils to get paste? --> <version_command>make-consensi.py --version</version_command> <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' > '$output' </command> @@ -21,14 +20,14 @@ <test> <param name="fastq1" value="smoke_1.fq"/> <param name="fastq2" value="smoke_2.fq"/> - <param name="taglen" value="5"/> + <param name="taglen" value="4"/> <param name="invariant" value="1"/> <output name="output" file="smoke.families.tsv"/> </test> <test> <param name="fastq1" value="smoke_1.fq"/> <param name="fastq2" value="smoke_2.fq"/> - <param name="taglen" value="5"/> + <param name="taglen" value="4"/> <param name="invariant" value="0"/> <output name="output" file="smoke.families.i0.tsv"/> </test>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out.log Wed Feb 16 22:59:00 2022 +0000 @@ -0,0 +1,1698 @@ +git --git-dir /home/me/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' +git --git-dir /home/me/.planemo/gx_repo config remote.origin.mirror true +git --git-dir /home/me/.planemo/gx_repo remote update >/dev/null 2>&1 +git clone --branch master /home/me/.planemo/gx_repo /tmp/tmppmuqm8bo/galaxy-dev +if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} +Activated a virtualenv for Galaxy +/home/me/.planemo/gx_venv_3 +Set COMMON_STARTUP_ARGS to --dev-wheels +Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample +Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample +Initializing static/welcome.html from welcome.html.sample +Activating virtualenv at /home/me/.planemo/gx_venv_3 +Requirement already satisfied: pip>=19.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (20.0.2) +Ignoring async-exit-stack: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring async-generator: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring atomicwrites: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring cached-property: markers 'python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring cffi: markers 'implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")' don't match your environment +Ignoring colorama: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0"' don't match your environment +Ignoring contextvars: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring dataclasses: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring immutables: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring importlib-metadata: markers 'python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8")' don't match your environment +Ignoring importlib-resources: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring py: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.4.0" and python_version >= "3.6" and implementation_name == "pypy"' don't match your environment +Ignoring pycparser: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32" and python_version >= "3.8"' don't match your environment +Ignoring pyreadline: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" and sys_platform == "win32" or python_version >= "3.6" and python_version < "3.8" and python_full_version >= "3.5.0" and sys_platform == "win32"' don't match your environment +Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring typing-extensions: markers 'python_version >= "3.6" and python_version < "3.8"' don't match your environment +Ignoring zipp: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple +Requirement already satisfied: adal==1.2.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (1.2.7) +Requirement already satisfied: aiofiles==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.6.0) +Requirement already satisfied: alabaster==0.7.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (0.7.12) +Requirement already satisfied: amqp==5.0.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 6)) (5.0.6) +Requirement already satisfied: appdirs==1.4.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 7)) (1.4.4) +Requirement already satisfied: argcomplete==1.12.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (1.12.3) +Requirement already satisfied: attmap==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (0.13.0) +Requirement already satisfied: attrs==20.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (20.3.0) +Requirement already satisfied: babel==2.9.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (2.9.0) +Requirement already satisfied: bagit-profile==1.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 15)) (1.3.1) +Requirement already satisfied: bagit==1.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (1.8.1) +Requirement already satisfied: bcrypt==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (3.2.0) +Requirement already satisfied: bdbag==1.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (1.6.1) +Requirement already satisfied: beaker==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 19)) (1.11.0) +Requirement already satisfied: billiard==3.6.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (3.6.4.0) +Requirement already satisfied: bioblend==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (0.15.0) +Requirement already satisfied: bleach==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (3.3.0) +Requirement already satisfied: boltons==20.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 23)) (20.2.1) +Requirement already satisfied: boto3==1.16.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (1.16.63) +Requirement already satisfied: boto==2.49.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 25)) (2.49.0) +Requirement already satisfied: botocore==1.19.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.19.63) +Requirement already satisfied: bx-python==0.8.11 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.8.11) +Requirement already satisfied: cachecontrol==0.11.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.11.7) +Requirement already satisfied: cachetools==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (4.2.2) +Requirement already satisfied: celery==5.0.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 31)) (5.0.5) +Requirement already satisfied: certifi==2020.12.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (2020.12.5) +Requirement already satisfied: chardet==4.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (4.0.0) +Requirement already satisfied: cheetah3==3.2.6.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (3.2.6.post1) +Requirement already satisfied: circus==0.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 36)) (0.17.1) +Requirement already satisfied: click-didyoumean==0.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (0.0.3) +Requirement already satisfied: click-plugins==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.1.1) +Requirement already satisfied: click-repl==0.1.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (0.1.6) +Requirement already satisfied: click==7.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (7.1.2) +Requirement already satisfied: cliff==3.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (3.7.0) +Requirement already satisfied: cloudauthz==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.6.0) +Requirement already satisfied: cloudbridge==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (2.1.0) +Requirement already satisfied: cmd2==1.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.5.0) +Requirement already satisfied: coloredlogs==15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (15.0) +Requirement already satisfied: commonmark==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (0.9.1) +Requirement already satisfied: coverage==5.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (5.5) +Requirement already satisfied: cryptography==3.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 50)) (3.4.7) +Requirement already satisfied: cwltool==3.0.20201109103151 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (3.0.20201109103151) +Requirement already satisfied: debtcollector==2.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (2.2.0) +Requirement already satisfied: decorator==5.0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (5.0.7) +Requirement already satisfied: defusedxml==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.7.1) +Requirement already satisfied: deprecated==1.2.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.2.12) +Requirement already satisfied: deprecation==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (0.4) +Requirement already satisfied: docopt==0.6.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (0.6.2) +Requirement already satisfied: docutils==0.16 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.16) +Requirement already satisfied: dogpile.cache==1.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (1.1.2) +Requirement already satisfied: ecdsa==0.14.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (0.14.1) +Requirement already satisfied: edam-ontology==1.25.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (1.25.2) +Requirement already satisfied: fabric3==1.14.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (1.14.post1) +Requirement already satisfied: fastapi-utils==0.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 65)) (0.2.1) +Requirement already satisfied: fastapi==0.65.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 66)) (0.65.2) +Requirement already satisfied: fluent-logger==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (0.10.0) +Requirement already satisfied: fs==2.4.13 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 68)) (2.4.13) +Requirement already satisfied: funcsigs==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 69)) (1.0.2) +Requirement already satisfied: future==0.18.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 70)) (0.18.2) +Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 71)) (1.1.5) +Requirement already satisfied: google-api-core==1.26.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 72)) (1.26.3) +Requirement already satisfied: google-api-python-client==1.12.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 73)) (1.12.8) +Requirement already satisfied: google-auth-httplib2==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 74)) (0.1.0) +Requirement already satisfied: google-auth==1.30.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 75)) (1.30.0) +Requirement already satisfied: googleapis-common-protos==1.53.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 76)) (1.53.0) +Requirement already satisfied: greenlet==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 77)) (1.0.0) +Requirement already satisfied: gunicorn==20.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 78)) (20.1.0) +Requirement already satisfied: gxformat2==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 79)) (0.15.0) +Requirement already satisfied: h11==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 80)) (0.12.0) +Requirement already satisfied: h5py==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 81)) (3.1.0) +Requirement already satisfied: httpcore==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 82)) (0.13.0) +Requirement already satisfied: httplib2==0.19.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 83)) (0.19.1) +Requirement already satisfied: httpx==0.18.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 84)) (0.18.0) +Requirement already satisfied: humanfriendly==9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 85)) (9.1) +Requirement already satisfied: idna==2.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 86)) (2.10) +Requirement already satisfied: imagesize==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 87)) (1.2.0) +Requirement already satisfied: iniconfig==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 91)) (1.1.1) +Requirement already satisfied: isa-rwval==0.10.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 92)) (0.10.10) +Requirement already satisfied: iso8601==0.1.14 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 93)) (0.1.14) +Requirement already satisfied: isodate==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 94)) (0.6.0) +Requirement already satisfied: jinja2==2.11.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 95)) (2.11.3) +Requirement already satisfied: jmespath==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 96)) (0.10.0) +Requirement already satisfied: jsonpatch==1.32 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 97)) (1.32) +Requirement already satisfied: jsonpointer==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 98)) (2.1) +Requirement already satisfied: jsonschema==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 99)) (3.2.0) +Requirement already satisfied: keystoneauth1==4.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 100)) (4.3.1) +Requirement already satisfied: kombu==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 101)) (5.0.2) +Requirement already satisfied: lagom==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 102)) (1.2.0) +Requirement already satisfied: lockfile==0.12.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 103)) (0.12.2) +Requirement already satisfied: lxml==4.6.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 104)) (4.6.3) +Requirement already satisfied: mako==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 105)) (1.1.4) +Requirement already satisfied: markdown-it-reporter==0.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 106)) (0.0.2) +Requirement already satisfied: markdown==3.3.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 107)) (3.3.4) +Requirement already satisfied: markupsafe==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 108)) (1.1.1) +Requirement already satisfied: mercurial==5.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 109)) (5.7.1) +Requirement already satisfied: mirakuru==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 110)) (2.3.0) +Requirement already satisfied: mistune==0.8.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 111)) (0.8.4) +Requirement already satisfied: mrcfile==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 112)) (1.3.0) +Requirement already satisfied: msgpack==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 113)) (1.0.2) +Requirement already satisfied: munch==2.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 114)) (2.5.0) +Requirement already satisfied: mypy-extensions==0.4.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 115)) (0.4.3) +Requirement already satisfied: netaddr==0.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 116)) (0.8.0) +Requirement already satisfied: netifaces==0.10.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 117)) (0.10.9) +Requirement already satisfied: networkx==2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 118)) (2.5) +Requirement already satisfied: nodeenv==1.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 119)) (1.6.0) +Requirement already satisfied: nose==1.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 120)) (1.3.7) +Requirement already satisfied: nosehtml==0.4.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 121)) (0.4.6) +Requirement already satisfied: numpy==1.19.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 122)) (1.19.5) +Requirement already satisfied: oauth2client==4.1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 123)) (4.1.3) +Requirement already satisfied: oauthlib==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 124)) (3.1.0) +Requirement already satisfied: openstacksdk==0.52.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 125)) (0.52.0) +Requirement already satisfied: os-client-config==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 126)) (2.1.0) +Requirement already satisfied: os-service-types==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 127)) (1.7.0) +Requirement already satisfied: osc-lib==2.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 128)) (2.3.1) +Requirement already satisfied: oslo.config==8.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 129)) (8.6.0) +Requirement already satisfied: oslo.context==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 130)) (3.2.0) +Requirement already satisfied: oslo.i18n==5.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 131)) (5.0.1) +Requirement already satisfied: oslo.log==4.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 132)) (4.4.0) +Requirement already satisfied: oslo.serialization==4.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 133)) (4.1.0) +Requirement already satisfied: oslo.utils==4.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 134)) (4.8.0) +Requirement already satisfied: oyaml==1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 135)) (1.0) +Requirement already satisfied: packaging==20.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 136)) (20.9) +Requirement already satisfied: paramiko==2.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 137)) (2.7.2) +Requirement already satisfied: parsley==1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 138)) (1.3) +Requirement already satisfied: paste==3.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 139)) (3.5.0) +Requirement already satisfied: pastedeploy==2.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 140)) (2.1.1) +Requirement already satisfied: pbr==5.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 141)) (5.6.0) +Requirement already satisfied: pluggy==0.13.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 142)) (0.13.1) +Requirement already satisfied: port-for==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 143)) (0.4) +Requirement already satisfied: prettytable==0.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 144)) (0.7.2) +Requirement already satisfied: prompt-toolkit==3.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 145)) (3.0.3) +Requirement already satisfied: protobuf==3.15.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 146)) (3.15.8) +Requirement already satisfied: prov==1.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 147)) (1.5.1) +Requirement already satisfied: psutil==5.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 148)) (5.8.0) +Requirement already satisfied: pulsar-galaxy-lib==0.14.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 149)) (0.14.10) +Requirement already satisfied: pyasn1-modules==0.2.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 151)) (0.2.8) +Requirement already satisfied: pyasn1==0.4.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 152)) (0.4.8) +Requirement already satisfied: pycryptodome==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 154)) (3.10.1) +Requirement already satisfied: pydantic==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 155)) (1.8.2) +Requirement already satisfied: pydot==1.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 156)) (1.4.2) +Requirement already satisfied: pyeventsystem==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 157)) (0.1.0) +Requirement already satisfied: pyfaidx==0.5.9.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 158)) (0.5.9.5) +Requirement already satisfied: pygithub==1.55 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 159)) (1.55) +Requirement already satisfied: pygments==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 160)) (2.8.1) +Requirement already satisfied: pyinotify==0.9.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 161)) (0.9.6) +Requirement already satisfied: pyjwt==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 162)) (2.1.0) +Requirement already satisfied: pykwalify==1.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 163)) (1.8.0) +Requirement already satisfied: pynacl==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 164)) (1.4.0) +Requirement already satisfied: pyparsing==2.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 165)) (2.4.7) +Requirement already satisfied: pyperclip==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 166)) (1.8.2) +Requirement already satisfied: pyrsistent==0.17.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 169)) (0.17.3) +Requirement already satisfied: pysam==0.16.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 170)) (0.16.0.1) +Requirement already satisfied: pytest-asyncio==0.15.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 171)) (0.15.1) +Requirement already satisfied: pytest-cov==2.11.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 172)) (2.11.1) +Requirement already satisfied: pytest-html==3.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 173)) (3.1.1) +Requirement already satisfied: pytest-json-report==1.2.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 174)) (1.2.4) +Requirement already satisfied: pytest-metadata==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 175)) (1.11.0) +Requirement already satisfied: pytest-mock==3.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 176)) (3.6.0) +Requirement already satisfied: pytest-postgresql==2.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 177)) (2.6.1) +Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 178)) (0.7.3) +Requirement already satisfied: pytest-shard==0.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 179)) (0.1.2) +Requirement already satisfied: pytest==6.2.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (6.2.3) +Requirement already satisfied: python-dateutil==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 181)) (2.8.1) +Requirement already satisfied: python-irodsclient==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 182)) (1.0.0) +Requirement already satisfied: python-jose==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 183)) (3.2.0) +Requirement already satisfied: python-keystoneclient==4.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 184)) (4.1.1) +Requirement already satisfied: python-neutronclient==7.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 185)) (7.2.1) +Requirement already satisfied: python-novaclient==17.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 186)) (17.2.1) +Requirement already satisfied: python-swiftclient==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 187)) (3.10.1) +Requirement already satisfied: python3-openid==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 188)) (3.2.0) +Requirement already satisfied: pytz==2021.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 189)) (2021.1) +Requirement already satisfied: pyuwsgi==2.0.19.1.post0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 190)) (2.0.19.1.post0) +Requirement already satisfied: pyyaml==5.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 191)) (5.4.1) +Requirement already satisfied: pyzmq==22.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 192)) (22.0.3) +Requirement already satisfied: rdflib-jsonld==0.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 193)) (0.5.0) +Requirement already satisfied: rdflib==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 194)) (4.2.2) +Requirement already satisfied: recommonmark==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 195)) (0.7.1) +Requirement already satisfied: refgenconf==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (0.12.0) +Requirement already satisfied: repoze.lru==0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 197)) (0.7) +Requirement already satisfied: requests-oauthlib==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 198)) (1.3.0) +Requirement already satisfied: requests-toolbelt==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 199)) (0.9.1) +Requirement already satisfied: requests==2.25.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 200)) (2.25.1) +Requirement already satisfied: requestsexceptions==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 201)) (1.4.0) +Requirement already satisfied: responses==0.13.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 202)) (0.13.3) +Requirement already satisfied: rfc3986==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 203)) (1.4.0) +Requirement already satisfied: routes==2.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 204)) (2.5.1) +Requirement already satisfied: rsa==4.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 205)) (4.7.2) +Requirement already satisfied: ruamel.yaml==0.16.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 207)) (0.16.5) +Requirement already satisfied: s3transfer==0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 208)) (0.3.7) +Requirement already satisfied: schema-salad==7.1.20210316164414 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 209)) (7.1.20210316164414) +Requirement already satisfied: selenium==3.141.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 210)) (3.141.0) +Requirement already satisfied: setuptools-scm==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 211)) (5.0.2) +Requirement already satisfied: shellescape==3.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 212)) (3.4.1) +Requirement already satisfied: simplejson==3.17.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 213)) (3.17.2) +Requirement already satisfied: six==1.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 214)) (1.15.0) +Requirement already satisfied: sniffio==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 215)) (1.2.0) +Requirement already satisfied: snowballstemmer==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 216)) (2.1.0) +Requirement already satisfied: social-auth-core==4.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 217)) (4.0.3) +Requirement already satisfied: sortedcontainers==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 218)) (2.3.0) +Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 219)) (0.0.15) +Requirement already satisfied: sphinx-rtd-theme==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 220)) (0.5.2) +Requirement already satisfied: sphinx==3.5.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 221)) (3.5.4) +Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 222)) (1.0.2) +Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 223)) (1.0.2) +Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 224)) (1.0.3) +Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 225)) (1.0.1) +Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 226)) (1.0.3) +Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 227)) (1.1.4) +Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 228)) (0.13.0) +Requirement already satisfied: sqlalchemy==1.4.20 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 229)) (1.4.20) +Requirement already satisfied: sqlitedict==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 230)) (1.7.0) +Requirement already satisfied: sqlparse==0.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 231)) (0.4.2) +Requirement already satisfied: starlette-context==0.3.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 232)) (0.3.2) +Requirement already satisfied: starlette==0.14.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 233)) (0.14.2) +Requirement already satisfied: statsd==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 234)) (3.3.0) +Requirement already satisfied: stevedore==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 235)) (3.3.0) +Requirement already satisfied: svgwrite==1.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 236)) (1.4.1) +Requirement already satisfied: tempita==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 237)) (0.5.2) +Requirement already satisfied: tenacity==7.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 238)) (7.0.0) +Requirement already satisfied: testfixtures==6.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 239)) (6.17.1) +Requirement already satisfied: tifffile==2020.9.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 240)) (2020.9.3) +Requirement already satisfied: toml==0.10.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 241)) (0.10.2) +Requirement already satisfied: tornado==6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 242)) (6.1) +Requirement already satisfied: tqdm==4.60.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 243)) (4.60.0) +Requirement already satisfied: twill==3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 244)) (3.0) +Requirement already satisfied: tzlocal==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 246)) (2.1) +Requirement already satisfied: ubiquerg==0.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 247)) (0.6.1) +Requirement already satisfied: unidecode==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 248)) (1.2.0) +Requirement already satisfied: uritemplate==3.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 249)) (3.0.1) +Requirement already satisfied: urllib3==1.26.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 250)) (1.26.4) +Requirement already satisfied: uvicorn==0.13.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 251)) (0.13.4) +Requirement already satisfied: vine==5.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 252)) (5.0.0) +Requirement already satisfied: watchdog==2.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 253)) (2.0.3) +Requirement already satisfied: wcwidth==0.2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 254)) (0.2.5) +Requirement already satisfied: webencodings==0.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 255)) (0.5.1) +Requirement already satisfied: webob==1.8.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 256)) (1.8.7) +Requirement already satisfied: whoosh==2.7.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 257)) (2.7.4) +Requirement already satisfied: wrapt==1.12.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 258)) (1.12.1) +Requirement already satisfied: xmlrunner==1.7.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 259)) (1.7.7) +Requirement already satisfied: yacman==0.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 260)) (0.8.2) +Requirement already satisfied: zipstream-new==1.1.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 262)) (1.1.8) +Requirement already satisfied: cffi>=1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (1.15.0) +Requirement already satisfied: colorama>=0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cmd2==1.5.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.4.4) +Requirement already satisfied: setuptools in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (44.0.0) +Requirement already satisfied: typing-extensions in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (4.1.1) +Requirement already satisfied: py>=1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from pytest==6.2.3->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (1.11.0) +Requirement already satisfied: rich>=9.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from refgenconf==0.12.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (11.2.0) +Requirement already satisfied: pycparser in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cffi>=1.1->bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (2.21) +The Galaxy client has not yet been built and will be built now. +yarn install v1.22.17 +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +Done in 39.03s. +yarn run v1.22.17 +$ NODE_ENV=production gulp && yarn run webpack-production-maps && yarn run save-build-hash +[16:13:41] Using gulpfile /tmp/tmppmuqm8bo/galaxy-dev/client/gulpfile.js +[16:13:41] Starting 'default'... +[16:13:41] Starting 'fonts'... +[16:13:41] Starting 'stageLibs'... +[16:13:41] Starting 'buildPlugins'... +[16:13:41] Finished 'stageLibs' after 14 ms +[16:13:41] Finished 'buildPlugins' after 17 ms +[16:13:41] Starting 'cleanPlugins'... +[16:13:41] Finished 'fonts' after 26 ms +No build hashfile detected for annotate_image, generating now. +Installing Dependencies for annotate_image +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building annotate_image +$ parcel build src/script.js -d static --no-source-maps +✨ Built in 7.86s. + +static/script.js 424.02 KB 7.56s +No build hashfile detected for chiraviz, generating now. +Installing Dependencies for chiraviz +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building chiraviz +$ webpack --mode production +Hash: a9bccc156676dbe85389 +Version: webpack 4.46.0 +Time: 1555ms +Built at: 02/16/2022 4:14:20 PM + Asset Size Chunks Chunk Names +448c34a56d699c29117adc64c43affeb.woff2 17.6 KiB [emitted] + 674f50d287a8c48dc19ba404d20fe713.eot 162 KiB [emitted] + 89889688147bd7575d6327160d64e760.svg 106 KiB [emitted] + 912ec66d7572ff821749319396470bde.svg 434 KiB [emitted] [big] +af7ae505a9eed503f8b8e6982036873e.woff2 75.4 KiB [emitted] + b06871f281fee6b241d60582ae9369b9.ttf 162 KiB [emitted] + e18bbf611f2a2e43afc071aa2f4e1512.ttf 44.3 KiB [emitted] + f4769f9bdb7466be65088239c12046d1.eot 19.7 KiB [emitted] + fa2772327f55d8198301fdb8bcfc8158.woff 22.9 KiB [emitted] + fee66e712a8a08eef5805a46892932ad.woff 95.7 KiB [emitted] + images/plus-icon.png 2.6 KiB [emitted] + images/search-icon.png 9.78 KiB [emitted] + main.css 153 KiB 0 [emitted] main + script.js 3.72 MiB 0 [emitted] [big] main +Entrypoint main [big] = main.css script.js + [1] ./src/index.js 390 bytes {0} [built] + [4] ./node_modules/script-loader!./src/js/rna-viz.js 318 bytes {0} [built] + [5] ./node_modules/raw-loader!./src/js/rna-viz.js 56.8 KiB {0} [built] +[10] ./node_modules/script-loader!./src/js/visualize-alignment.js 330 bytes {0} [built] +[11] ./node_modules/raw-loader!./src/js/visualize-alignment.js 4.8 KiB {0} [built] +[16] ./src/css/rna.viz.css 39 bytes {0} [built] + + 14 hidden modules + +WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB). +This can impact web performance. +Assets: + 912ec66d7572ff821749319396470bde.svg (434 KiB) + script.js (3.72 MiB) + +WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance. +Entrypoints: + main (3.87 MiB) + main.css + script.js + + +WARNING in webpack performance recommendations: +You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application. +For more info visit https://webpack.js.org/guides/code-splitting/ +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/bootstrap/dist/css/bootstrap.min.css: + Entrypoint mini-css-extract-plugin = * + 8 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/font-awesome/css/font-awesome.min.css: + Entrypoint mini-css-extract-plugin = * + 9 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!src/css/rna.viz.css: + Entrypoint mini-css-extract-plugin = * + [0] ./node_modules/css-loader/dist/cjs.js!./src/css/rna.viz.css 4.61 KiB {0} [built] + + 1 hidden module +No build hashfile detected for editor, generating now. +Installing Dependencies for editor +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building editor +$ webpack --mode production +Hash: 0049facab9a1a81ab2fd +Version: webpack 4.46.0 +Time: 3135ms +Built at: 02/16/2022 4:14:29 PM + Asset Size Chunks Chunk Names + main.css 777 bytes 0 [emitted] main +script.js 394 KiB 0 [emitted] [big] main +Entrypoint main [big] = main.css script.js +[0] (webpack)/buildin/module.js 497 bytes {0} [built] +[1] (webpack)/buildin/amd-define.js 85 bytes {0} [built] +[2] ./src/index.js 172 bytes {0} [built] +[3] ./src/styles/style.css 39 bytes {0} [built] + + 4 hidden modules + +WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB). +This can impact web performance. +Assets: + script.js (394 KiB) + +WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance. +Entrypoints: + main (395 KiB) + main.css + script.js + + +WARNING in webpack performance recommendations: +You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application. +For more info visit https://webpack.js.org/guides/code-splitting/ +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!src/styles/style.css: + Entrypoint mini-css-extract-plugin = * + [0] ./node_modules/css-loader/dist/cjs.js!./src/styles/style.css 1.03 KiB {0} [built] + + 1 hidden module +No build hashfile detected for heatmap_default, generating now. +Installing Dependencies for heatmap_default +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building heatmap_default +$ parcel build src/script.js -d static/dist +✨ Built in 9.16s. + +static/dist/script.js.map ⚠️ 1.21 MB 84ms +static/dist/script.js 360.29 KB 8.74s +No build hashfile detected for hyphyvision, generating now. +Installing Dependencies for hyphyvision +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building hyphyvision +$ webpack --mode development +Hash: 439618303504b8033e69 +Version: webpack 4.46.0 +Time: 2757ms +Built at: 02/16/2022 4:15:01 PM + Asset Size Chunks Chunk Names + main.css 272 KiB main [emitted] main +script.js 5.66 MiB main [emitted] main +Entrypoint main = main.css script.js +[./node_modules/webpack/buildin/amd-define.js] (webpack)/buildin/amd-define.js 85 bytes {main} [built] +[./node_modules/webpack/buildin/amd-options.js] (webpack)/buildin/amd-options.js 80 bytes {main} [built] +[./node_modules/webpack/buildin/global.js] (webpack)/buildin/global.js 472 bytes {main} [built] +[./node_modules/webpack/buildin/module.js] (webpack)/buildin/module.js 497 bytes {main} [built] +[./src/index.js] 215 bytes {main} [built] + + 99 hidden modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/hyphy-vision/dist/hyphyvision.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/phylotree/phylotree.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +No build hashfile detected for media_player, generating now. +Installing Dependencies for media_player +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building media_player +$ cp node_modules/plyr/dist/plyr.js node_modules/plyr/dist/plyr.css static/dist +No build hashfile detected for mvpapp, generating now. +Installing Dependencies for mvpapp +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building mvpapp +$ webpack --mode production +Hash: a018669153ba50c870db +Version: webpack 4.46.0 +Time: 3504ms +Built at: 02/16/2022 4:15:14 PM + Asset Size Chunks Chunk Names + 0417cf0d391d231809b74bc884265e55.png 757 bytes [emitted] + 0b708185ce8927f18c7b3b82a7e7c247.png 278 bytes [emitted] + 1173aff0adae43093a9489d25d461d8b.png 738 bytes [emitted] + 23932de7c235b03187b8a5de3d024490.png 5.68 KiB [emitted] + 2f257489d9600ddf56d195a179ebc9df.png 4.44 KiB [emitted] + 448c34a56d699c29117adc64c43affeb.woff2 17.6 KiB [emitted] + 4c27b34156b7a3776f31cc456ca01c10.png 6.76 KiB [emitted] + 4d4e638960a1a29b0d6b693b445087da.png 418 bytes [emitted] + 53acc69aaee6e2cb73b2021317e24af3.png 328 bytes [emitted] + 635a2c6439e2a8a51a6c2ff50a6da089.png 3.04 KiB [emitted] + 6686d21b904e18b100210169bb1c04ad.png 4.44 KiB [emitted] + 772a64d6df4b93d230e9b38e1ab7522a.png 4.44 KiB [emitted] + 89889688147bd7575d6327160d64e760.svg 106 KiB [emitted] + 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+Entrypoint main [big] = script.js + [4] ./src/index.js 160 KiB {0} [built] + [5] ./src/js/publicPath.js 276 bytes {0} [built] + [6] ./src/css/jquery-ui.min.css 533 bytes {0} [built] +[22] ./src/css/lorikeet.css 528 bytes {0} [built] +[27] ./src/css/datatables.min.css 534 bytes {0} [built] +[29] ./src/css/msi.css 523 bytes {0} [built] +[31] ./src/css/app.css 523 bytes {0} [built] +[33] ./src/css/igv.css 523 bytes {0} [built] +[42] ./node_modules/script-loader!./src/js/jquery.min.js 315 bytes {0} [built] +[44] ./node_modules/script-loader!./src/js/jquery-ui.min.js 318 bytes {0} [built] +[59] ./node_modules/script-loader!./src/js/popper.min.js 315 bytes {0} [built] +[61] ./node_modules/script-loader!./src/js/plotly-latest.min.js 322 bytes {0} [built] +[63] ./node_modules/script-loader!./src/js/datatables.min.js 319 bytes {0} [built] +[65] ./node_modules/script-loader!./src/js/d3.min.js 311 bytes {0} [built] +[69] ./node_modules/script-loader!./src/js/msms_graphs.js 316 bytes {0} [built] + + 56 hidden modules +No build hashfile detected for ngl, generating now. +Installing Dependencies for ngl +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building ngl +$ parcel build src/ngl.js -d static/dist +✨ Built in 15.21s. + +static/dist/ngl.js.map ⚠️ 2.1 MB 185ms +static/dist/ngl.js 958.08 KB 14.68s +No build hashfile detected for nora, generating now. +Installing Dependencies for nora +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building nora +$ cpy --cwd='node_modules/@galaxyproject/nora/static/dist' --parents './' '../../../../../static/dist' +No build hashfile detected for openlayers, generating now. +Installing Dependencies for openlayers +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building openlayers +$ parcel build src/script.js -d static --no-source-maps +npm WARN deprecated babel-preset-es2015@6.24.1: 🙌 Thanks for using Babel: we recommend using babel-preset-env now: please read https://babeljs.io/env to update! +npm WARN deprecated core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +npm WARN lifecycle The node binary used for scripts is /tmp/yarn--1645046156281-0.770431282331616/node but npm is using /home/me/.planemo/gx_venv_3/bin/node itself. Use the `--scripts-prepend-node-path` option to include the path for the node binary npm was executed with. + +> core-js@2.6.12 postinstall /tmp/tmppmuqm8bo/galaxy-dev/config/plugins/visualizations/openlayers/node_modules/wkt-parser/node_modules/core-js +> node -e "try{require('./postinstall')}catch(e){}" + +npm notice created a lockfile as package-lock.json. You should commit this file. ++ babel-preset-es2015@6.24.1 +added 66 packages from 14 contributors and audited 66 packages in 3.191s +found 0 vulnerabilities + +⚠️ Could not infer babel version. Defaulting to babel 7. Please add either babel-core or @babel/core as a dependency. ++ @babel/core@7.17.4 +added 52 packages from 62 contributors and audited 118 packages in 2.34s + +3 packages are looking for funding + run `npm fund` for details + +found 0 vulnerabilities + +✨ Built in 20.60s. + +static/script.js ⚠️ 1.33 MB 20.27s +No build hashfile detected for openseadragon, generating now. +Installing Dependencies for openseadragon +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building openseadragon +$ cpy --cwd='node_modules/openseadragon/build/openseadragon' --parents './' '../../../../static/dist' +No build hashfile detected for pv, generating now. +Installing Dependencies for pv +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building pv +$ parcel build 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[big] vendors~workflowLayout + vendors~workflowLayout.chunk.js.map 3.71 MiB 14 [emitted] [dev] vendors~workflowLayout + workflowLayout.chunk.js 1.5 KiB 15 [emitted] workflowLayout + workflowLayout.chunk.js.map 4.37 KiB 15 [emitted] [dev] workflowLayout +Entrypoint login [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map login.bundled.js login.bundled.js.map +Entrypoint analysis [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map analysis.bundled.js analysis.bundled.js.map +Entrypoint admin [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map admin.bundled.js admin.bundled.js.map +Entrypoint generic [big] = base.css base.chunk.js base.chunk.js.map libs.chunk.js libs.chunk.js.map generic.bundled.js generic.bundled.js.map + [1] ./node_modules/underscore/modules/index-all.js + 1 modules 326 bytes {0} [built] + | 2 modules + [15] ./src/utils/utils.js 10.4 KiB {7} {8} {9} {10} [built] + [52] 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[built] +[1860] multi polyfills bundleEntries entry/analysis 52 bytes {8} [built] +[2219] multi polyfills bundleEntries entry/admin 52 bytes {7} [built] +[2226] multi polyfills bundleEntries entry/generic 52 bytes {9} [built] +[2227] ./src/entry/generic.js 122 bytes {9} [built] +[2336] ./src/entry/analysis/index.js + 576 modules 924 KiB {8} [built] + | ./src/entry/analysis/index.js 1.18 KiB [built] + | ./src/entry/analysis/AnalysisRouter.js 20.1 KiB [built] + | ./src/entry/panels/tool-panel.js 1.11 KiB [built] + | ./src/entry/panels/history-panel.js 3.74 KiB [built] + | ./src/mvc/grid/grid-shared.js 2.2 KiB [built] + | ./src/mvc/history/history-list.js 4.25 KiB [built] + | ../static/plugins/welcome_page/new_user/dist/static/topics/index.js 289 bytes [built] + | ./src/mvc/history/options-menu.js 6.67 KiB [built] + | ./src/mvc/history/history-view-edit-current.js 18.5 KiB [built] + | ../static/plugins/welcome_page/new_user/dist/static/topics/scripts/combine.js 107 bytes [built] + | ./src/mvc/entrypoints/poll.js 823 bytes [built] + | ./src/utils/observable/whenAny.js 468 bytes [built] + | ./src/utils/math.js 103 bytes [built] + | ./src/utils/validation.js 542 bytes [built] + | ./src/utils/observable/index.js 897 bytes [built] + | + 562 hidden modules +[2337] ./src/entry/admin/index.js + 253 modules 272 KiB {7} [built] + | ./src/entry/admin/index.js 692 bytes [built] + | ./src/entry/admin/AdminRouter.js 7.85 KiB [built] + | ./src/entry/panels/admin-panel.js 5.03 KiB [built] + | + 251 hidden modules +[2338] ./src/entry/login/index.js + 15 modules 14.6 KiB {10} [built] + | ./src/entry/login/index.js 1.07 KiB [built] + | + 15 hidden modules + + 3072 hidden modules + +WARNING in ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& (./node_modules/babel-loader/lib??ref--2!./node_modules/vue-loader/lib??vue-loader-options!./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js&) 40:16-26 +"export 'JobMetrics' was not found in 'components/JobMetrics/JobMetrics' + @ ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& + @ ./src/components/JobInformation/JobDetails.vue + @ ./src/entry/analysis/AnalysisRouter.js + @ ./src/entry/analysis/index.js + @ multi polyfills bundleEntries entry/analysis + +WARNING in ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& (./node_modules/babel-loader/lib??ref--2!./node_modules/vue-loader/lib??vue-loader-options!./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js&) 41:19-32 +"export 'JobParameters' was not found in 'components/JobParameters/JobParameters' + @ ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& + @ ./src/components/JobInformation/JobDetails.vue + @ ./src/entry/analysis/AnalysisRouter.js + @ ./src/entry/analysis/index.js + @ multi polyfills bundleEntries entry/analysis + +WARNING in chunk base [mini-css-extract-plugin] +Conflicting order. Following module has been added: + * css ./node_modules/css-loader/dist/cjs.js??ref--8-1!./node_modules/vue-loader/lib/loaders/stylePostLoader.js!./node_modules/postcss-loader/src??ref--8-2!./node_modules/sass-loader/dist/cjs.js??ref--8-3!./node_modules/vue-loader/lib??vue-loader-options!./src/components/Collections/common/ClickToEdit.vue?vue&type=style&index=0&lang=css& +despite it was not able to fulfill desired ordering with these modules: + * css ./node_modules/css-loader/dist/cjs.js??ref--8-1!./node_modules/vue-loader/lib/loaders/stylePostLoader.js!./node_modules/postcss-loader/src??ref--8-2!./node_modules/sass-loader/dist/cjs.js??ref--8-3!./node_modules/vue-loader/lib??vue-loader-options!./src/components/Collections/UnpairedDatasetElementView.vue?vue&type=style&index=0&lang=css& + - couldn't fulfill desired order of chunk group(s) PairedListCollectionCreator + - while fulfilling desired order of chunk group(s) analysis + +WARNING in core-js + Multiple versions of core-js found: + 2.6.5 ./~/@babel/polyfill/~/core-js + 3.18.3 ./~/core-js + + +WARNING in es-abstract + Multiple versions of es-abstract found: + 1.17.7 ./~/regexp.prototype.flags/~/es-abstract + 1.18.0-next.1 ./~/es-abstract + + +WARNING in isarray + Multiple versions of isarray found: + 1.0.0 ./~/isarray + 2.0.5 ./~/deep-equal/~/isarray + + +WARNING in lodash + Multiple versions of lodash found: + 4.17.11 ./~/vueisotope/~/lodash + 4.17.20 ./~/lodash + + +WARNING in object-keys + Multiple versions of object-keys found: + 1.0.12 ./~/define-properties/~/object-keys + 1.1.1 ./~/object-keys + + +WARNING in tslib + Multiple versions of tslib found: + 1.13.0 ./~/tslib + 1.9.3 ./~/rxjs/~/tslib + +Check how you can resolve duplicate packages: +https://github.com/darrenscerri/duplicate-package-checker-webpack-plugin#resolving-duplicate-packages-in-your-bundle + + +WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB). +This can impact web performance. +Assets: + CacheWorker.worker.bundled.worker.js (943 KiB) + assets/3c45c98f6f6c1b009c082510d0255ef4.svg (699 KiB) + assets/18df003f90a7f1313b98b23384ec4f1b.svg (876 KiB) + libs.chunk.js (3.35 MiB) + base.css (2.89 MiB) + admin.bundled.js (2.26 MiB) + analysis.bundled.js (2.77 MiB) + generic.bundled.js (2.08 MiB) + login.bundled.js (2.11 MiB) + vendors~Screenshot.chunk.js (340 KiB) + vendors~ruleCollectionBuilder.chunk.js (621 KiB) + vendors~workflowLayout.chunk.js (1.27 MiB) + base.css.map (7.35 MiB) + +WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance. +Entrypoints: + login (8.34 MiB) + base.css + base.chunk.js + libs.chunk.js + login.bundled.js + analysis (9 MiB) + base.css + base.chunk.js + libs.chunk.js + analysis.bundled.js + admin (8.5 MiB) + base.css + base.chunk.js + libs.chunk.js + admin.bundled.js + generic (8.32 MiB) + base.css + base.chunk.js + libs.chunk.js + generic.bundled.js + +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/splitpanes/dist/splitpanes.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/vue-multiselect/dist/vue-multiselect.min.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!src/components/History/ContentItem/styles.scss: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!src/components/History/adapters/HistoryPanelProxy.scss: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!src/style/scss/base.scss: + Entrypoint mini-css-extract-plugin = * + [0] ./node_modules/css-loader/dist/cjs.js??ref--8-1!./node_modules/postcss-loader/src??ref--8-2!./node_modules/sass-loader/dist/cjs.js??ref--8-3!./src/style/scss/base.scss 2.92 MiB {0} [built] + [18] 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mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/handsontable/dist/handsontable.full.css?vue&type=style&index=0&lang=css&: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/vue-loader/lib/index.js??vue-loader-options!src/components/Citation/Citation.vue?vue&type=style&index=0&lang=css&: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin 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2>/dev/null || echo '') >../static/client_build_hash.txt +Done in 382.17s. +/tmp/tmppmuqm8bo/galaxy-dev +Starting Galaxy with command [cd /tmp/tmppmuqm8bo/galaxy-dev && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && /tmp/tmppmuqm8bo/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --server-name main] +Activated a virtualenv for Galaxy +/home/me/.planemo/gx_venv_3 +Set COMMON_STARTUP_ARGS to --dev-wheels +Activating virtualenv at /home/me/.planemo/gx_venv_3 +Requirement already satisfied: pip>=19.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (20.0.2) +Ignoring async-exit-stack: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring async-generator: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring atomicwrites: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring cached-property: markers 'python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring cffi: markers 'implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")' don't match your environment +Ignoring colorama: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0"' don't match your environment +Ignoring contextvars: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring dataclasses: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring immutables: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring importlib-metadata: markers 'python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8")' don't match your environment +Ignoring importlib-resources: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring py: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.4.0" and python_version >= "3.6" and implementation_name == "pypy"' don't match your environment +Ignoring pycparser: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32" and python_version >= "3.8"' don't match your environment +Ignoring pyreadline: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" and sys_platform == "win32" or python_version >= "3.6" and python_version < "3.8" and python_full_version >= "3.5.0" and sys_platform == "win32"' don't match your environment +Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring typing-extensions: markers 'python_version >= "3.6" and python_version < "3.8"' don't match your environment +Ignoring zipp: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple +Requirement already satisfied: adal==1.2.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (1.2.7) +Requirement already satisfied: aiofiles==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.6.0) +Requirement already satisfied: alabaster==0.7.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (0.7.12) +Requirement already satisfied: amqp==5.0.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 6)) (5.0.6) +Requirement already satisfied: appdirs==1.4.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 7)) (1.4.4) +Requirement already satisfied: argcomplete==1.12.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (1.12.3) +Requirement already satisfied: attmap==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (0.13.0) +Requirement already satisfied: attrs==20.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (20.3.0) +Requirement already satisfied: babel==2.9.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (2.9.0) +Requirement already satisfied: bagit-profile==1.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 15)) (1.3.1) +Requirement already satisfied: bagit==1.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (1.8.1) +Requirement already satisfied: bcrypt==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (3.2.0) +Requirement already satisfied: bdbag==1.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (1.6.1) +Requirement already satisfied: beaker==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 19)) (1.11.0) +Requirement already satisfied: billiard==3.6.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (3.6.4.0) +Requirement already satisfied: bioblend==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (0.15.0) +Requirement already satisfied: bleach==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (3.3.0) +Requirement already satisfied: boltons==20.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 23)) (20.2.1) +Requirement already satisfied: boto3==1.16.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (1.16.63) +Requirement already satisfied: boto==2.49.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 25)) (2.49.0) +Requirement already satisfied: botocore==1.19.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.19.63) +Requirement already satisfied: bx-python==0.8.11 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.8.11) +Requirement already satisfied: cachecontrol==0.11.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.11.7) +Requirement already satisfied: cachetools==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (4.2.2) +Requirement already satisfied: celery==5.0.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 31)) (5.0.5) +Requirement already satisfied: certifi==2020.12.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (2020.12.5) +Requirement already satisfied: chardet==4.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (4.0.0) +Requirement already satisfied: cheetah3==3.2.6.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (3.2.6.post1) +Requirement already satisfied: circus==0.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 36)) (0.17.1) +Requirement already satisfied: click-didyoumean==0.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (0.0.3) +Requirement already satisfied: click-plugins==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.1.1) +Requirement already satisfied: click-repl==0.1.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (0.1.6) +Requirement already satisfied: click==7.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (7.1.2) +Requirement already satisfied: cliff==3.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (3.7.0) +Requirement already satisfied: cloudauthz==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.6.0) +Requirement already satisfied: cloudbridge==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (2.1.0) +Requirement already satisfied: cmd2==1.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.5.0) +Requirement already satisfied: coloredlogs==15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (15.0) +Requirement already satisfied: commonmark==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (0.9.1) +Requirement already satisfied: coverage==5.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (5.5) +Requirement already satisfied: cryptography==3.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 50)) (3.4.7) +Requirement already satisfied: cwltool==3.0.20201109103151 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (3.0.20201109103151) +Requirement already satisfied: debtcollector==2.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (2.2.0) +Requirement already satisfied: decorator==5.0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (5.0.7) +Requirement already satisfied: defusedxml==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.7.1) +Requirement already satisfied: deprecated==1.2.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.2.12) +Requirement already satisfied: deprecation==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (0.4) +Requirement already satisfied: docopt==0.6.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (0.6.2) +Requirement already satisfied: docutils==0.16 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.16) +Requirement already satisfied: dogpile.cache==1.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (1.1.2) +Requirement already satisfied: ecdsa==0.14.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (0.14.1) +Requirement already satisfied: edam-ontology==1.25.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (1.25.2) +Requirement already satisfied: fabric3==1.14.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (1.14.post1) +Requirement already satisfied: fastapi-utils==0.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 65)) (0.2.1) +Requirement already satisfied: fastapi==0.65.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 66)) (0.65.2) +Requirement already satisfied: fluent-logger==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (0.10.0) +Requirement already satisfied: fs==2.4.13 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 68)) (2.4.13) +Requirement already satisfied: funcsigs==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 69)) (1.0.2) +Requirement already satisfied: future==0.18.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 70)) (0.18.2) +Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 71)) (1.1.5) +Requirement already satisfied: google-api-core==1.26.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 72)) (1.26.3) +Requirement already satisfied: google-api-python-client==1.12.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 73)) (1.12.8) +Requirement already satisfied: google-auth-httplib2==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 74)) (0.1.0) +Requirement already satisfied: google-auth==1.30.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 75)) (1.30.0) +Requirement already satisfied: googleapis-common-protos==1.53.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 76)) (1.53.0) +Requirement already satisfied: greenlet==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 77)) (1.0.0) +Requirement already satisfied: gunicorn==20.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 78)) (20.1.0) +Requirement already satisfied: gxformat2==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 79)) (0.15.0) +Requirement already satisfied: h11==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 80)) (0.12.0) +Requirement already satisfied: h5py==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 81)) (3.1.0) +Requirement already satisfied: httpcore==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 82)) (0.13.0) +Requirement already satisfied: httplib2==0.19.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 83)) (0.19.1) +Requirement already satisfied: httpx==0.18.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 84)) (0.18.0) +Requirement already satisfied: humanfriendly==9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 85)) (9.1) +Requirement already satisfied: idna==2.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 86)) (2.10) +Requirement already satisfied: imagesize==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 87)) (1.2.0) +Requirement already satisfied: iniconfig==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 91)) (1.1.1) +Requirement already satisfied: isa-rwval==0.10.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 92)) (0.10.10) +Requirement already satisfied: iso8601==0.1.14 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 93)) (0.1.14) +Requirement already satisfied: isodate==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 94)) (0.6.0) +Requirement already satisfied: jinja2==2.11.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 95)) (2.11.3) +Requirement already satisfied: jmespath==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 96)) (0.10.0) +Requirement already satisfied: jsonpatch==1.32 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 97)) (1.32) +Requirement already satisfied: jsonpointer==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 98)) (2.1) +Requirement already satisfied: jsonschema==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 99)) (3.2.0) +Requirement already satisfied: keystoneauth1==4.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 100)) (4.3.1) +Requirement already satisfied: kombu==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 101)) (5.0.2) +Requirement already satisfied: lagom==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 102)) (1.2.0) +Requirement already satisfied: lockfile==0.12.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 103)) (0.12.2) +Requirement already satisfied: lxml==4.6.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 104)) (4.6.3) +Requirement already satisfied: mako==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 105)) (1.1.4) +Requirement already satisfied: markdown-it-reporter==0.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 106)) (0.0.2) +Requirement already satisfied: markdown==3.3.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 107)) (3.3.4) +Requirement already satisfied: markupsafe==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 108)) (1.1.1) +Requirement already satisfied: mercurial==5.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 109)) (5.7.1) +Requirement already satisfied: mirakuru==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 110)) (2.3.0) +Requirement already satisfied: mistune==0.8.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 111)) (0.8.4) +Requirement already satisfied: mrcfile==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 112)) (1.3.0) +Requirement already satisfied: msgpack==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 113)) (1.0.2) +Requirement already satisfied: munch==2.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 114)) (2.5.0) +Requirement already satisfied: mypy-extensions==0.4.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 115)) (0.4.3) +Requirement already satisfied: netaddr==0.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 116)) (0.8.0) +Requirement already satisfied: netifaces==0.10.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 117)) (0.10.9) +Requirement already satisfied: networkx==2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 118)) (2.5) +Requirement already satisfied: nodeenv==1.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 119)) (1.6.0) +Requirement already satisfied: nose==1.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 120)) (1.3.7) +Requirement already satisfied: nosehtml==0.4.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 121)) (0.4.6) +Requirement already satisfied: numpy==1.19.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 122)) (1.19.5) +Requirement already satisfied: oauth2client==4.1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 123)) (4.1.3) +Requirement already satisfied: oauthlib==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 124)) (3.1.0) +Requirement already satisfied: openstacksdk==0.52.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 125)) (0.52.0) +Requirement already satisfied: os-client-config==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 126)) (2.1.0) +Requirement already satisfied: os-service-types==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 127)) (1.7.0) +Requirement already satisfied: osc-lib==2.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 128)) (2.3.1) +Requirement already satisfied: oslo.config==8.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 129)) (8.6.0) +Requirement already satisfied: oslo.context==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 130)) (3.2.0) +Requirement already satisfied: oslo.i18n==5.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 131)) (5.0.1) +Requirement already satisfied: oslo.log==4.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 132)) (4.4.0) +Requirement already satisfied: oslo.serialization==4.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 133)) (4.1.0) +Requirement already satisfied: oslo.utils==4.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 134)) (4.8.0) +Requirement already satisfied: oyaml==1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 135)) (1.0) +Requirement already satisfied: packaging==20.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 136)) (20.9) +Requirement already satisfied: paramiko==2.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 137)) (2.7.2) +Requirement already satisfied: parsley==1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 138)) (1.3) +Requirement already satisfied: paste==3.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 139)) (3.5.0) +Requirement already satisfied: pastedeploy==2.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 140)) (2.1.1) +Requirement already satisfied: pbr==5.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 141)) (5.6.0) +Requirement already satisfied: pluggy==0.13.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 142)) (0.13.1) +Requirement already satisfied: port-for==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 143)) (0.4) +Requirement already satisfied: prettytable==0.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 144)) (0.7.2) +Requirement already satisfied: prompt-toolkit==3.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 145)) (3.0.3) +Requirement already satisfied: protobuf==3.15.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 146)) (3.15.8) +Requirement already satisfied: prov==1.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 147)) (1.5.1) +Requirement already satisfied: psutil==5.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 148)) (5.8.0) +Requirement already satisfied: pulsar-galaxy-lib==0.14.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 149)) (0.14.10) +Requirement already satisfied: pyasn1-modules==0.2.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 151)) (0.2.8) +Requirement already satisfied: pyasn1==0.4.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 152)) (0.4.8) +Requirement already satisfied: pycryptodome==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 154)) (3.10.1) +Requirement already satisfied: pydantic==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 155)) (1.8.2) +Requirement already satisfied: pydot==1.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 156)) (1.4.2) +Requirement already satisfied: pyeventsystem==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 157)) (0.1.0) +Requirement already satisfied: pyfaidx==0.5.9.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 158)) (0.5.9.5) +Requirement already satisfied: pygithub==1.55 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 159)) (1.55) +Requirement already satisfied: pygments==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 160)) (2.8.1) +Requirement already satisfied: pyinotify==0.9.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 161)) (0.9.6) +Requirement already satisfied: pyjwt==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 162)) (2.1.0) +Requirement already satisfied: pykwalify==1.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 163)) (1.8.0) +Requirement already satisfied: pynacl==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 164)) (1.4.0) +Requirement already satisfied: pyparsing==2.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 165)) (2.4.7) +Requirement already satisfied: pyperclip==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 166)) (1.8.2) +Requirement already satisfied: pyrsistent==0.17.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 169)) (0.17.3) +Requirement already satisfied: pysam==0.16.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 170)) (0.16.0.1) +Requirement already satisfied: pytest-asyncio==0.15.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 171)) (0.15.1) +Requirement already satisfied: pytest-cov==2.11.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 172)) (2.11.1) +Requirement already satisfied: pytest-html==3.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 173)) (3.1.1) +Requirement already satisfied: pytest-json-report==1.2.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 174)) (1.2.4) +Requirement already satisfied: pytest-metadata==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 175)) (1.11.0) +Requirement already satisfied: pytest-mock==3.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 176)) (3.6.0) +Requirement already satisfied: pytest-postgresql==2.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 177)) (2.6.1) +Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 178)) (0.7.3) +Requirement already satisfied: pytest-shard==0.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 179)) (0.1.2) +Requirement already satisfied: pytest==6.2.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (6.2.3) +Requirement already satisfied: python-dateutil==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 181)) (2.8.1) +Requirement already satisfied: python-irodsclient==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 182)) (1.0.0) +Requirement already satisfied: python-jose==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 183)) (3.2.0) +Requirement already satisfied: python-keystoneclient==4.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 184)) (4.1.1) +Requirement already satisfied: python-neutronclient==7.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 185)) (7.2.1) +Requirement already satisfied: python-novaclient==17.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 186)) (17.2.1) +Requirement already satisfied: python-swiftclient==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 187)) (3.10.1) +Requirement already satisfied: python3-openid==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 188)) (3.2.0) +Requirement already satisfied: pytz==2021.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 189)) (2021.1) +Requirement already satisfied: pyuwsgi==2.0.19.1.post0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 190)) (2.0.19.1.post0) +Requirement already satisfied: pyyaml==5.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 191)) (5.4.1) +Requirement already satisfied: pyzmq==22.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 192)) (22.0.3) +Requirement already satisfied: rdflib-jsonld==0.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 193)) (0.5.0) +Requirement already satisfied: rdflib==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 194)) (4.2.2) +Requirement already satisfied: recommonmark==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 195)) (0.7.1) +Requirement already satisfied: refgenconf==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (0.12.0) +Requirement already satisfied: repoze.lru==0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 197)) (0.7) +Requirement already satisfied: requests-oauthlib==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 198)) (1.3.0) +Requirement already satisfied: requests-toolbelt==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 199)) (0.9.1) +Requirement already satisfied: requests==2.25.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 200)) (2.25.1) +Requirement already satisfied: requestsexceptions==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 201)) (1.4.0) +Requirement already satisfied: responses==0.13.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 202)) (0.13.3) +Requirement already satisfied: rfc3986==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 203)) (1.4.0) +Requirement already satisfied: routes==2.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 204)) (2.5.1) +Requirement already satisfied: rsa==4.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 205)) (4.7.2) +Requirement already satisfied: ruamel.yaml==0.16.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 207)) (0.16.5) +Requirement already satisfied: s3transfer==0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 208)) (0.3.7) +Requirement already satisfied: schema-salad==7.1.20210316164414 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 209)) (7.1.20210316164414) +Requirement already satisfied: selenium==3.141.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 210)) (3.141.0) +Requirement already satisfied: setuptools-scm==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 211)) (5.0.2) +Requirement already satisfied: shellescape==3.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 212)) (3.4.1) +Requirement already satisfied: simplejson==3.17.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 213)) (3.17.2) +Requirement already satisfied: six==1.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 214)) (1.15.0) +Requirement already satisfied: sniffio==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 215)) (1.2.0) +Requirement already satisfied: snowballstemmer==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 216)) (2.1.0) +Requirement already satisfied: social-auth-core==4.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 217)) (4.0.3) +Requirement already satisfied: sortedcontainers==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 218)) (2.3.0) +Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 219)) (0.0.15) +Requirement already satisfied: sphinx-rtd-theme==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 220)) (0.5.2) +Requirement already satisfied: sphinx==3.5.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 221)) (3.5.4) +Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 222)) (1.0.2) +Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 223)) (1.0.2) +Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 224)) (1.0.3) +Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 225)) (1.0.1) +Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 226)) (1.0.3) +Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 227)) (1.1.4) +Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 228)) (0.13.0) +Requirement already satisfied: sqlalchemy==1.4.20 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 229)) (1.4.20) +Requirement already satisfied: sqlitedict==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 230)) (1.7.0) +Requirement already satisfied: sqlparse==0.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 231)) (0.4.2) +Requirement already satisfied: starlette-context==0.3.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 232)) (0.3.2) +Requirement already satisfied: starlette==0.14.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 233)) (0.14.2) +Requirement already satisfied: statsd==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 234)) (3.3.0) +Requirement already satisfied: stevedore==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 235)) (3.3.0) +Requirement already satisfied: svgwrite==1.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 236)) (1.4.1) +Requirement already satisfied: tempita==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 237)) (0.5.2) +Requirement already satisfied: tenacity==7.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 238)) (7.0.0) +Requirement already satisfied: testfixtures==6.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 239)) (6.17.1) +Requirement already satisfied: tifffile==2020.9.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 240)) (2020.9.3) +Requirement already satisfied: toml==0.10.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 241)) (0.10.2) +Requirement already satisfied: tornado==6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 242)) (6.1) +Requirement already satisfied: tqdm==4.60.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 243)) (4.60.0) +Requirement already satisfied: twill==3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 244)) (3.0) +Requirement already satisfied: tzlocal==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 246)) (2.1) +Requirement already satisfied: ubiquerg==0.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 247)) (0.6.1) +Requirement already satisfied: unidecode==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 248)) (1.2.0) +Requirement already satisfied: uritemplate==3.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 249)) (3.0.1) +Requirement already satisfied: urllib3==1.26.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 250)) (1.26.4) +Requirement already satisfied: uvicorn==0.13.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 251)) (0.13.4) +Requirement already satisfied: vine==5.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 252)) (5.0.0) +Requirement already satisfied: watchdog==2.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 253)) (2.0.3) +Requirement already satisfied: wcwidth==0.2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 254)) (0.2.5) +Requirement already satisfied: webencodings==0.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 255)) (0.5.1) +Requirement already satisfied: webob==1.8.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 256)) (1.8.7) +Requirement already satisfied: whoosh==2.7.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 257)) (2.7.4) +Requirement already satisfied: wrapt==1.12.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 258)) (1.12.1) +Requirement already satisfied: xmlrunner==1.7.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 259)) (1.7.7) +Requirement already satisfied: yacman==0.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 260)) (0.8.2) +Requirement already satisfied: zipstream-new==1.1.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 262)) (1.1.8) +Requirement already satisfied: cffi>=1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (1.15.0) +Requirement already satisfied: colorama>=0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cmd2==1.5.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.4.4) +Requirement already satisfied: setuptools in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (44.0.0) +Requirement already satisfied: typing-extensions in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (4.1.1) +Requirement already satisfied: py>=1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from pytest==6.2.3->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (1.11.0) +Requirement already satisfied: rich>=9.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from refgenconf==0.12.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (11.2.0) +Requirement already satisfied: pycparser in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cffi>=1.1->bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (2.21) +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Requirement already satisfied: watchdog in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r /dev/stdin (line 1)) (2.0.3) +The Galaxy client build is up to date and will not be rebuilt at this time. +Activating virtualenv at /home/me/.planemo/gx_venv_3 +Executing: gunicorn --pythonpath lib --paste "/tmp/tmppmuqm8bo/galaxy.ini"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out2.log Wed Feb 16 22:59:00 2022 +0000 @@ -0,0 +1,1704 @@ +git --git-dir /home/me/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' +git --git-dir /home/me/.planemo/gx_repo config remote.origin.mirror true +git --git-dir /home/me/.planemo/gx_repo remote update >/dev/null 2>&1 +git clone --branch master /home/me/.planemo/gx_repo /tmp/tmp1upz926i/galaxy-dev +if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} +Activated a virtualenv for Galaxy +/home/me/.planemo/gx_venv_3 +Set COMMON_STARTUP_ARGS to --dev-wheels +Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample +Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample +Initializing static/welcome.html from welcome.html.sample +Activating virtualenv at /home/me/.planemo/gx_venv_3 +Requirement already satisfied: pip>=19.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (20.0.2) +Ignoring async-exit-stack: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring async-generator: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring atomicwrites: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring cached-property: markers 'python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring cffi: markers 'implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")' don't match your environment +Ignoring colorama: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0"' don't match your environment +Ignoring contextvars: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring dataclasses: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring immutables: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring importlib-metadata: markers 'python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8")' don't match your environment +Ignoring importlib-resources: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring py: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.4.0" and python_version >= "3.6" and implementation_name == "pypy"' don't match your environment +Ignoring pycparser: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32" and python_version >= "3.8"' don't match your environment +Ignoring pyreadline: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" and sys_platform == "win32" or python_version >= "3.6" and python_version < "3.8" and python_full_version >= "3.5.0" and sys_platform == "win32"' don't match your environment +Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring typing-extensions: markers 'python_version >= "3.6" and python_version < "3.8"' don't match your environment +Ignoring zipp: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple +Requirement already satisfied: adal==1.2.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (1.2.7) +Requirement already satisfied: aiofiles==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.6.0) +Requirement already satisfied: alabaster==0.7.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (0.7.12) +Requirement already satisfied: amqp==5.0.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 6)) (5.0.6) +Requirement already satisfied: appdirs==1.4.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 7)) (1.4.4) +Requirement already satisfied: argcomplete==1.12.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (1.12.3) +Requirement already satisfied: attmap==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (0.13.0) +Requirement already satisfied: attrs==20.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (20.3.0) +Requirement already satisfied: babel==2.9.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (2.9.0) +Requirement already satisfied: bagit-profile==1.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 15)) (1.3.1) +Requirement already satisfied: bagit==1.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (1.8.1) +Requirement already satisfied: bcrypt==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (3.2.0) +Requirement already satisfied: bdbag==1.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (1.6.1) +Requirement already satisfied: beaker==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 19)) (1.11.0) +Requirement already satisfied: billiard==3.6.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (3.6.4.0) +Requirement already satisfied: bioblend==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (0.15.0) +Requirement already satisfied: bleach==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (3.3.0) +Requirement already satisfied: boltons==20.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 23)) (20.2.1) +Requirement already satisfied: boto3==1.16.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (1.16.63) +Requirement already satisfied: boto==2.49.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 25)) (2.49.0) +Requirement already satisfied: botocore==1.19.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.19.63) +Requirement already satisfied: bx-python==0.8.11 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.8.11) +Requirement already satisfied: cachecontrol==0.11.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.11.7) +Requirement already satisfied: cachetools==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (4.2.2) +Requirement already satisfied: celery==5.0.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 31)) (5.0.5) +Requirement already satisfied: certifi==2020.12.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (2020.12.5) +Requirement already satisfied: chardet==4.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (4.0.0) +Requirement already satisfied: cheetah3==3.2.6.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (3.2.6.post1) +Requirement already satisfied: circus==0.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 36)) (0.17.1) +Requirement already satisfied: click-didyoumean==0.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (0.0.3) +Requirement already satisfied: click-plugins==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.1.1) +Requirement already satisfied: click-repl==0.1.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (0.1.6) +Requirement already satisfied: click==7.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (7.1.2) +Requirement already satisfied: cliff==3.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (3.7.0) +Requirement already satisfied: cloudauthz==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.6.0) +Requirement already satisfied: cloudbridge==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (2.1.0) +Requirement already satisfied: cmd2==1.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.5.0) +Requirement already satisfied: coloredlogs==15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (15.0) +Requirement already satisfied: commonmark==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (0.9.1) +Requirement already satisfied: coverage==5.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (5.5) +Requirement already satisfied: cryptography==3.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 50)) (3.4.7) +Requirement already satisfied: cwltool==3.0.20201109103151 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (3.0.20201109103151) +Requirement already satisfied: debtcollector==2.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (2.2.0) +Requirement already satisfied: decorator==5.0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (5.0.7) +Requirement already satisfied: defusedxml==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.7.1) +Requirement already satisfied: deprecated==1.2.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.2.12) +Requirement already satisfied: deprecation==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (0.4) +Requirement already satisfied: docopt==0.6.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (0.6.2) +Requirement already satisfied: docutils==0.16 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.16) +Requirement already satisfied: dogpile.cache==1.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (1.1.2) +Requirement already satisfied: ecdsa==0.14.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (0.14.1) +Requirement already satisfied: edam-ontology==1.25.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (1.25.2) +Requirement already satisfied: fabric3==1.14.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (1.14.post1) +Requirement already satisfied: fastapi-utils==0.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 65)) (0.2.1) +Requirement already satisfied: fastapi==0.65.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 66)) (0.65.2) +Requirement already satisfied: fluent-logger==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (0.10.0) +Requirement already satisfied: fs==2.4.13 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 68)) (2.4.13) +Requirement already satisfied: funcsigs==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 69)) (1.0.2) +Requirement already satisfied: future==0.18.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 70)) (0.18.2) +Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 71)) (1.1.5) +Requirement already satisfied: google-api-core==1.26.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 72)) (1.26.3) +Requirement already satisfied: google-api-python-client==1.12.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 73)) (1.12.8) +Requirement already satisfied: google-auth-httplib2==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 74)) (0.1.0) +Requirement already satisfied: google-auth==1.30.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 75)) (1.30.0) +Requirement already satisfied: googleapis-common-protos==1.53.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 76)) (1.53.0) +Requirement already satisfied: greenlet==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 77)) (1.0.0) +Requirement already satisfied: gunicorn==20.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 78)) (20.1.0) +Requirement already satisfied: gxformat2==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 79)) (0.15.0) +Requirement already satisfied: h11==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 80)) (0.12.0) +Requirement already satisfied: h5py==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 81)) (3.1.0) +Requirement already satisfied: httpcore==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 82)) (0.13.0) +Requirement already satisfied: httplib2==0.19.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 83)) (0.19.1) +Requirement already satisfied: httpx==0.18.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 84)) (0.18.0) +Requirement already satisfied: humanfriendly==9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 85)) (9.1) +Requirement already satisfied: idna==2.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 86)) (2.10) +Requirement already satisfied: imagesize==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 87)) (1.2.0) +Requirement already satisfied: iniconfig==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 91)) (1.1.1) +Requirement already satisfied: isa-rwval==0.10.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 92)) (0.10.10) +Requirement already satisfied: iso8601==0.1.14 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 93)) (0.1.14) +Requirement already satisfied: isodate==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 94)) (0.6.0) +Requirement already satisfied: jinja2==2.11.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 95)) (2.11.3) +Requirement already satisfied: jmespath==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 96)) (0.10.0) +Requirement already satisfied: jsonpatch==1.32 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 97)) (1.32) +Requirement already satisfied: jsonpointer==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 98)) (2.1) +Requirement already satisfied: jsonschema==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 99)) (3.2.0) +Requirement already satisfied: keystoneauth1==4.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 100)) (4.3.1) +Requirement already satisfied: kombu==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 101)) (5.0.2) +Requirement already satisfied: lagom==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 102)) (1.2.0) +Requirement already satisfied: lockfile==0.12.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 103)) (0.12.2) +Requirement already satisfied: lxml==4.6.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 104)) (4.6.3) +Requirement already satisfied: mako==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 105)) (1.1.4) +Requirement already satisfied: markdown-it-reporter==0.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 106)) (0.0.2) +Requirement already satisfied: markdown==3.3.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 107)) (3.3.4) +Requirement already satisfied: markupsafe==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 108)) (1.1.1) +Requirement already satisfied: mercurial==5.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 109)) (5.7.1) +Requirement already satisfied: mirakuru==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 110)) (2.3.0) +Requirement already satisfied: mistune==0.8.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 111)) (0.8.4) +Requirement already satisfied: mrcfile==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 112)) (1.3.0) +Requirement already satisfied: msgpack==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 113)) (1.0.2) +Requirement already satisfied: munch==2.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 114)) (2.5.0) +Requirement already satisfied: mypy-extensions==0.4.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 115)) (0.4.3) +Requirement already satisfied: netaddr==0.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 116)) (0.8.0) +Requirement already satisfied: netifaces==0.10.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 117)) (0.10.9) +Requirement already satisfied: networkx==2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 118)) (2.5) +Requirement already satisfied: nodeenv==1.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 119)) (1.6.0) +Requirement already satisfied: nose==1.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 120)) (1.3.7) +Requirement already satisfied: nosehtml==0.4.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 121)) (0.4.6) +Requirement already satisfied: numpy==1.19.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 122)) (1.19.5) +Requirement already satisfied: oauth2client==4.1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 123)) (4.1.3) +Requirement already satisfied: oauthlib==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 124)) (3.1.0) +Requirement already satisfied: openstacksdk==0.52.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 125)) (0.52.0) +Requirement already satisfied: os-client-config==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 126)) (2.1.0) +Requirement already satisfied: os-service-types==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 127)) (1.7.0) +Requirement already satisfied: osc-lib==2.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 128)) (2.3.1) +Requirement already satisfied: oslo.config==8.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 129)) (8.6.0) +Requirement already satisfied: oslo.context==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 130)) (3.2.0) +Requirement already satisfied: oslo.i18n==5.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 131)) (5.0.1) +Requirement already satisfied: oslo.log==4.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 132)) (4.4.0) +Requirement already satisfied: oslo.serialization==4.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 133)) (4.1.0) +Requirement already satisfied: oslo.utils==4.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 134)) (4.8.0) +Requirement already satisfied: oyaml==1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 135)) (1.0) +Requirement already satisfied: packaging==20.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 136)) (20.9) +Requirement already satisfied: paramiko==2.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 137)) (2.7.2) +Requirement already satisfied: parsley==1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 138)) (1.3) +Requirement already satisfied: paste==3.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 139)) (3.5.0) +Requirement already satisfied: pastedeploy==2.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 140)) (2.1.1) +Requirement already satisfied: pbr==5.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 141)) (5.6.0) +Requirement already satisfied: pluggy==0.13.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 142)) (0.13.1) +Requirement already satisfied: port-for==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 143)) (0.4) +Requirement already satisfied: prettytable==0.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 144)) (0.7.2) +Requirement already satisfied: prompt-toolkit==3.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 145)) (3.0.3) +Requirement already satisfied: protobuf==3.15.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 146)) (3.15.8) +Requirement already satisfied: prov==1.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 147)) (1.5.1) +Requirement already satisfied: psutil==5.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 148)) (5.8.0) +Requirement already satisfied: pulsar-galaxy-lib==0.14.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 149)) (0.14.10) +Requirement already satisfied: pyasn1-modules==0.2.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 151)) (0.2.8) +Requirement already satisfied: pyasn1==0.4.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 152)) (0.4.8) +Requirement already satisfied: pycryptodome==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 154)) (3.10.1) +Requirement already satisfied: pydantic==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 155)) (1.8.2) +Requirement already satisfied: pydot==1.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 156)) (1.4.2) +Requirement already satisfied: pyeventsystem==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 157)) (0.1.0) +Requirement already satisfied: pyfaidx==0.5.9.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 158)) (0.5.9.5) +Requirement already satisfied: pygithub==1.55 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 159)) (1.55) +Requirement already satisfied: pygments==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 160)) (2.8.1) +Requirement already satisfied: pyinotify==0.9.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 161)) (0.9.6) +Requirement already satisfied: pyjwt==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 162)) (2.1.0) +Requirement already satisfied: pykwalify==1.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 163)) (1.8.0) +Requirement already satisfied: pynacl==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 164)) (1.4.0) +Requirement already satisfied: pyparsing==2.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 165)) (2.4.7) +Requirement already satisfied: pyperclip==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 166)) (1.8.2) +Requirement already satisfied: pyrsistent==0.17.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 169)) (0.17.3) +Requirement already satisfied: pysam==0.16.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 170)) (0.16.0.1) +Requirement already satisfied: pytest-asyncio==0.15.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 171)) (0.15.1) +Requirement already satisfied: pytest-cov==2.11.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 172)) (2.11.1) +Requirement already satisfied: pytest-html==3.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 173)) (3.1.1) +Requirement already satisfied: pytest-json-report==1.2.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 174)) (1.2.4) +Requirement already satisfied: pytest-metadata==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 175)) (1.11.0) +Requirement already satisfied: pytest-mock==3.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 176)) (3.6.0) +Requirement already satisfied: pytest-postgresql==2.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 177)) (2.6.1) +Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 178)) (0.7.3) +Requirement already satisfied: pytest-shard==0.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 179)) (0.1.2) +Requirement already satisfied: pytest==6.2.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (6.2.3) +Requirement already satisfied: python-dateutil==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 181)) (2.8.1) +Requirement already satisfied: python-irodsclient==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 182)) (1.0.0) +Requirement already satisfied: python-jose==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 183)) (3.2.0) +Requirement already satisfied: python-keystoneclient==4.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 184)) (4.1.1) +Requirement already satisfied: python-neutronclient==7.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 185)) (7.2.1) +Requirement already satisfied: python-novaclient==17.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 186)) (17.2.1) +Requirement already satisfied: python-swiftclient==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 187)) (3.10.1) +Requirement already satisfied: python3-openid==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 188)) (3.2.0) +Requirement already satisfied: pytz==2021.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 189)) (2021.1) +Requirement already satisfied: pyuwsgi==2.0.19.1.post0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 190)) (2.0.19.1.post0) +Requirement already satisfied: pyyaml==5.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 191)) (5.4.1) +Requirement already satisfied: pyzmq==22.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 192)) (22.0.3) +Requirement already satisfied: rdflib-jsonld==0.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 193)) (0.5.0) +Requirement already satisfied: rdflib==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 194)) (4.2.2) +Requirement already satisfied: recommonmark==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 195)) (0.7.1) +Requirement already satisfied: refgenconf==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (0.12.0) +Requirement already satisfied: repoze.lru==0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 197)) (0.7) +Requirement already satisfied: requests-oauthlib==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 198)) (1.3.0) +Requirement already satisfied: requests-toolbelt==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 199)) (0.9.1) +Requirement already satisfied: requests==2.25.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 200)) (2.25.1) +Requirement already satisfied: requestsexceptions==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 201)) (1.4.0) +Requirement already satisfied: responses==0.13.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 202)) (0.13.3) +Requirement already satisfied: rfc3986==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 203)) (1.4.0) +Requirement already satisfied: routes==2.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 204)) (2.5.1) +Requirement already satisfied: rsa==4.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 205)) (4.7.2) +Requirement already satisfied: ruamel.yaml==0.16.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 207)) (0.16.5) +Requirement already satisfied: s3transfer==0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 208)) (0.3.7) +Requirement already satisfied: schema-salad==7.1.20210316164414 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 209)) (7.1.20210316164414) +Requirement already satisfied: selenium==3.141.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 210)) (3.141.0) +Requirement already satisfied: setuptools-scm==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 211)) (5.0.2) +Requirement already satisfied: shellescape==3.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 212)) (3.4.1) +Requirement already satisfied: simplejson==3.17.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 213)) (3.17.2) +Requirement already satisfied: six==1.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 214)) (1.15.0) +Requirement already satisfied: sniffio==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 215)) (1.2.0) +Requirement already satisfied: snowballstemmer==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 216)) (2.1.0) +Requirement already satisfied: social-auth-core==4.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 217)) (4.0.3) +Requirement already satisfied: sortedcontainers==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 218)) (2.3.0) +Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 219)) (0.0.15) +Requirement already satisfied: sphinx-rtd-theme==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 220)) (0.5.2) +Requirement already satisfied: sphinx==3.5.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 221)) (3.5.4) +Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 222)) (1.0.2) +Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 223)) (1.0.2) +Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 224)) (1.0.3) +Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 225)) (1.0.1) +Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 226)) (1.0.3) +Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 227)) (1.1.4) +Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 228)) (0.13.0) +Requirement already satisfied: sqlalchemy==1.4.20 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 229)) (1.4.20) +Requirement already satisfied: sqlitedict==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 230)) (1.7.0) +Requirement already satisfied: sqlparse==0.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 231)) (0.4.2) +Requirement already satisfied: starlette-context==0.3.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 232)) (0.3.2) +Requirement already satisfied: starlette==0.14.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 233)) (0.14.2) +Requirement already satisfied: statsd==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 234)) (3.3.0) +Requirement already satisfied: stevedore==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 235)) (3.3.0) +Requirement already satisfied: svgwrite==1.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 236)) (1.4.1) +Requirement already satisfied: tempita==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 237)) (0.5.2) +Requirement already satisfied: tenacity==7.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 238)) (7.0.0) +Requirement already satisfied: testfixtures==6.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 239)) (6.17.1) +Requirement already satisfied: tifffile==2020.9.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 240)) (2020.9.3) +Requirement already satisfied: toml==0.10.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 241)) (0.10.2) +Requirement already satisfied: tornado==6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 242)) (6.1) +Requirement already satisfied: tqdm==4.60.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 243)) (4.60.0) +Requirement already satisfied: twill==3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 244)) (3.0) +Requirement already satisfied: tzlocal==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 246)) (2.1) +Requirement already satisfied: ubiquerg==0.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 247)) (0.6.1) +Requirement already satisfied: unidecode==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 248)) (1.2.0) +Requirement already satisfied: uritemplate==3.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 249)) (3.0.1) +Requirement already satisfied: urllib3==1.26.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 250)) (1.26.4) +Requirement already satisfied: uvicorn==0.13.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 251)) (0.13.4) +Requirement already satisfied: vine==5.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 252)) (5.0.0) +Requirement already satisfied: watchdog==2.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 253)) (2.0.3) +Requirement already satisfied: wcwidth==0.2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 254)) (0.2.5) +Requirement already satisfied: webencodings==0.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 255)) (0.5.1) +Requirement already satisfied: webob==1.8.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 256)) (1.8.7) +Requirement already satisfied: whoosh==2.7.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 257)) (2.7.4) +Requirement already satisfied: wrapt==1.12.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 258)) (1.12.1) +Requirement already satisfied: xmlrunner==1.7.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 259)) (1.7.7) +Requirement already satisfied: yacman==0.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 260)) (0.8.2) +Requirement already satisfied: zipstream-new==1.1.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 262)) (1.1.8) +Requirement already satisfied: cffi>=1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (1.15.0) +Requirement already satisfied: colorama>=0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cmd2==1.5.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.4.4) +Requirement already satisfied: typing-extensions in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (4.1.1) +Requirement already satisfied: setuptools in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (44.0.0) +Requirement already satisfied: py>=1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from pytest==6.2.3->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (1.11.0) +Requirement already satisfied: rich>=9.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from refgenconf==0.12.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (11.2.0) +Requirement already satisfied: pycparser in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cffi>=1.1->bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (2.21) +The Galaxy client has not yet been built and will be built now. +yarn install v1.22.17 +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +Done in 41.34s. +yarn run v1.22.17 +$ NODE_ENV=production gulp && yarn run webpack-production-maps && yarn run save-build-hash +[17:13:01] Using gulpfile /tmp/tmp1upz926i/galaxy-dev/client/gulpfile.js +[17:13:01] Starting 'default'... +[17:13:01] Starting 'fonts'... +[17:13:01] Starting 'stageLibs'... +[17:13:01] Starting 'buildPlugins'... +[17:13:01] Finished 'stageLibs' after 14 ms +[17:13:01] Finished 'buildPlugins' after 17 ms +[17:13:01] Starting 'cleanPlugins'... +[17:13:01] Finished 'fonts' after 26 ms +No build hashfile detected for annotate_image, generating now. +Installing Dependencies for annotate_image +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building annotate_image +$ parcel build src/script.js -d static --no-source-maps +✨ Built in 8.69s. + +static/script.js 424.02 KB 8.36s +No build hashfile detected for chiraviz, generating now. +Installing Dependencies for chiraviz +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building chiraviz +$ webpack --mode production +Hash: bc470bafb6d4fa387752 +Version: webpack 4.46.0 +Time: 1529ms +Built at: 02/16/2022 5:13:30 PM + Asset Size Chunks Chunk Names +448c34a56d699c29117adc64c43affeb.woff2 17.6 KiB [emitted] + 674f50d287a8c48dc19ba404d20fe713.eot 162 KiB [emitted] + 89889688147bd7575d6327160d64e760.svg 106 KiB [emitted] + 912ec66d7572ff821749319396470bde.svg 434 KiB [emitted] [big] +af7ae505a9eed503f8b8e6982036873e.woff2 75.4 KiB [emitted] + b06871f281fee6b241d60582ae9369b9.ttf 162 KiB [emitted] + e18bbf611f2a2e43afc071aa2f4e1512.ttf 44.3 KiB [emitted] + f4769f9bdb7466be65088239c12046d1.eot 19.7 KiB [emitted] + fa2772327f55d8198301fdb8bcfc8158.woff 22.9 KiB [emitted] + fee66e712a8a08eef5805a46892932ad.woff 95.7 KiB [emitted] + images/plus-icon.png 2.6 KiB [emitted] + images/search-icon.png 9.78 KiB [emitted] + main.css 153 KiB 0 [emitted] main + script.js 3.72 MiB 0 [emitted] [big] main +Entrypoint main [big] = main.css script.js + [1] ./src/index.js 390 bytes {0} [built] + [4] ./node_modules/script-loader!./src/js/rna-viz.js 318 bytes {0} [built] + [5] ./node_modules/raw-loader!./src/js/rna-viz.js 56.8 KiB {0} [built] +[10] ./node_modules/script-loader!./src/js/visualize-alignment.js 330 bytes {0} [built] +[11] ./node_modules/raw-loader!./src/js/visualize-alignment.js 4.8 KiB {0} [built] +[16] ./src/css/rna.viz.css 39 bytes {0} [built] + + 14 hidden modules + +WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB). +This can impact web performance. +Assets: + 912ec66d7572ff821749319396470bde.svg (434 KiB) + script.js (3.72 MiB) + +WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance. +Entrypoints: + main (3.87 MiB) + main.css + script.js + + +WARNING in webpack performance recommendations: +You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application. +For more info visit https://webpack.js.org/guides/code-splitting/ +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/bootstrap/dist/css/bootstrap.min.css: + Entrypoint mini-css-extract-plugin = * + 8 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/font-awesome/css/font-awesome.min.css: + Entrypoint mini-css-extract-plugin = * + 9 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!src/css/rna.viz.css: + Entrypoint mini-css-extract-plugin = * + [0] ./node_modules/css-loader/dist/cjs.js!./src/css/rna.viz.css 4.61 KiB {0} [built] + + 1 hidden module +No build hashfile detected for editor, generating now. +Installing Dependencies for editor +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building editor +$ webpack --mode production +Hash: 0049facab9a1a81ab2fd +Version: webpack 4.46.0 +Time: 3404ms +Built at: 02/16/2022 5:13:39 PM + Asset Size Chunks Chunk Names + main.css 777 bytes 0 [emitted] main +script.js 394 KiB 0 [emitted] [big] main +Entrypoint main [big] = main.css script.js +[0] (webpack)/buildin/module.js 497 bytes {0} [built] +[1] (webpack)/buildin/amd-define.js 85 bytes {0} [built] +[2] ./src/index.js 172 bytes {0} [built] +[3] ./src/styles/style.css 39 bytes {0} [built] + + 4 hidden modules + +WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB). +This can impact web performance. +Assets: + script.js (394 KiB) + +WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance. +Entrypoints: + main (395 KiB) + main.css + script.js + + +WARNING in webpack performance recommendations: +You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application. +For more info visit https://webpack.js.org/guides/code-splitting/ +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!src/styles/style.css: + Entrypoint mini-css-extract-plugin = * + [0] ./node_modules/css-loader/dist/cjs.js!./src/styles/style.css 1.03 KiB {0} [built] + + 1 hidden module +No build hashfile detected for heatmap_default, generating now. +Installing Dependencies for heatmap_default +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building heatmap_default +$ parcel build src/script.js -d static/dist +✨ Built in 9.07s. + +static/dist/script.js.map ⚠️ 1.21 MB 76ms +static/dist/script.js 360.29 KB 8.63s +No build hashfile detected for hyphyvision, generating now. +Installing Dependencies for hyphyvision +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building hyphyvision +$ webpack --mode development +Hash: 19951ee18264fd552b31 +Version: webpack 4.46.0 +Time: 2740ms +Built at: 02/16/2022 5:14:12 PM + Asset Size Chunks Chunk Names + main.css 272 KiB main [emitted] main +script.js 5.66 MiB main [emitted] main +Entrypoint main = main.css script.js +[./node_modules/webpack/buildin/amd-define.js] (webpack)/buildin/amd-define.js 85 bytes {main} [built] +[./node_modules/webpack/buildin/amd-options.js] (webpack)/buildin/amd-options.js 80 bytes {main} [built] +[./node_modules/webpack/buildin/global.js] (webpack)/buildin/global.js 472 bytes {main} [built] +[./node_modules/webpack/buildin/module.js] (webpack)/buildin/module.js 497 bytes {main} [built] +[./src/index.js] 215 bytes {main} [built] + + 99 hidden modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/hyphy-vision/dist/hyphyvision.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js!node_modules/phylotree/phylotree.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +No build hashfile detected for media_player, generating now. +Installing Dependencies for media_player +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building media_player +$ cp node_modules/plyr/dist/plyr.js node_modules/plyr/dist/plyr.css static/dist +No build hashfile detected for mvpapp, generating now. +Installing Dependencies for mvpapp +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building mvpapp +$ webpack --mode production +Hash: faa2020d31339c7d60cf +Version: webpack 4.46.0 +Time: 3441ms +Built at: 02/16/2022 5:14:24 PM + Asset Size Chunks Chunk Names + 0417cf0d391d231809b74bc884265e55.png 757 bytes [emitted] + 0b708185ce8927f18c7b3b82a7e7c247.png 278 bytes [emitted] + 1173aff0adae43093a9489d25d461d8b.png 738 bytes [emitted] + 23932de7c235b03187b8a5de3d024490.png 5.68 KiB [emitted] + 2f257489d9600ddf56d195a179ebc9df.png 4.44 KiB [emitted] + 448c34a56d699c29117adc64c43affeb.woff2 17.6 KiB [emitted] + 4c27b34156b7a3776f31cc456ca01c10.png 6.76 KiB [emitted] + 4d4e638960a1a29b0d6b693b445087da.png 418 bytes [emitted] + 53acc69aaee6e2cb73b2021317e24af3.png 328 bytes [emitted] + 635a2c6439e2a8a51a6c2ff50a6da089.png 3.04 KiB [emitted] + 6686d21b904e18b100210169bb1c04ad.png 4.44 KiB [emitted] + 772a64d6df4b93d230e9b38e1ab7522a.png 4.44 KiB [emitted] + 89889688147bd7575d6327160d64e760.svg 106 KiB [emitted] + a19fe1b2d726e920c12e43a65df9039a.png 6.15 KiB [emitted] + b624f702075cd719a38f428e143025ea.png 207 bytes [emitted] + c17f552e8f4697d7608c57653af36df0.png 262 bytes [emitted] + c31d5fc3eb7d82c628a82e3b87024cd1.png 205 bytes [emitted] + d0cc3ffc3dc84d3a7c48867c75e2485f.png 312 bytes [emitted] + e18bbf611f2a2e43afc071aa2f4e1512.ttf 44.3 KiB [emitted] + f4769f9bdb7466be65088239c12046d1.eot 19.7 KiB [emitted] + fa2772327f55d8198301fdb8bcfc8158.woff 22.9 KiB [emitted] + fe58c3539111d3021776e6833169c5e1.png 348 bytes [emitted] + images/header_lorikeet.png 11.3 KiB [emitted] + images/header_scan.png 3.6 KiB [emitted] + images/header_text.png 17.7 KiB [emitted] + images/lorikeet_text_small.png 3.38 KiB [emitted] + images/slider_handle.png 3.04 KiB [emitted] + images/sort_asc.png 160 bytes [emitted] + images/sort_asc_disabled.png 148 bytes [emitted] + images/sort_both.png 201 bytes [emitted] + images/sort_desc.png 158 bytes [emitted] + images/sort_desc_disabled.png 146 bytes [emitted] +images/ui-bg_diagonals-thick_18_b81900_40x40.png 418 bytes [emitted] +images/ui-bg_diagonals-thick_20_666666_40x40.png 312 bytes [emitted] + images/ui-bg_flat_10_000000_40x100.png 205 bytes [emitted] + images/ui-bg_glass_100_f6f6f6_1x400.png 262 bytes [emitted] + images/ui-bg_glass_100_fdf5ce_1x400.png 348 bytes [emitted] + images/ui-bg_glass_65_ffffff_1x400.png 207 bytes [emitted] + images/ui-bg_gloss-wave_35_f6a828_500x100.png 5.68 KiB [emitted] +images/ui-bg_highlight-soft_100_eeeeee_1x100.png 278 bytes [emitted] + images/ui-bg_highlight-soft_75_ffe45c_1x100.png 328 bytes [emitted] + images/ui-icons_222222_256x240.png 6.76 KiB [emitted] + images/ui-icons_228ef1_256x240.png 4.44 KiB [emitted] + images/ui-icons_ef8c08_256x240.png 4.44 KiB [emitted] + images/ui-icons_ffd27a_256x240.png 4.44 KiB [emitted] + images/ui-icons_ffffff_256x240.png 6.15 KiB [emitted] + images/zoom_in.png 757 bytes [emitted] + images/zoom_out.png 738 bytes [emitted] + script.js 5.44 MiB 0 [emitted] [big] main +Entrypoint main [big] = script.js + [4] ./src/index.js 160 KiB {0} [built] + [5] ./src/js/publicPath.js 276 bytes {0} [built] + [6] ./src/css/jquery-ui.min.css 533 bytes {0} [built] +[22] ./src/css/lorikeet.css 528 bytes {0} [built] +[27] ./src/css/datatables.min.css 534 bytes {0} [built] +[29] ./src/css/msi.css 523 bytes {0} [built] +[31] ./src/css/app.css 523 bytes {0} [built] +[33] ./src/css/igv.css 523 bytes {0} [built] +[42] ./node_modules/script-loader!./src/js/jquery.min.js 315 bytes {0} [built] +[44] ./node_modules/script-loader!./src/js/jquery-ui.min.js 318 bytes {0} [built] +[59] ./node_modules/script-loader!./src/js/popper.min.js 315 bytes {0} [built] +[61] ./node_modules/script-loader!./src/js/plotly-latest.min.js 322 bytes {0} [built] +[63] ./node_modules/script-loader!./src/js/datatables.min.js 319 bytes {0} [built] +[65] ./node_modules/script-loader!./src/js/d3.min.js 311 bytes {0} [built] +[69] ./node_modules/script-loader!./src/js/msms_graphs.js 316 bytes {0} [built] + + 56 hidden modules +No build hashfile detected for ngl, generating now. +Installing Dependencies for ngl +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building ngl +$ parcel build src/ngl.js -d static/dist +✨ Built in 16.25s. + +static/dist/ngl.js.map ⚠️ 2.1 MB 183ms +static/dist/ngl.js 958.08 KB 15.73s +No build hashfile detected for nora, generating now. +Installing Dependencies for nora +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building nora +$ cpy --cwd='node_modules/@galaxyproject/nora/static/dist' --parents './' '../../../../../static/dist' +No build hashfile detected for openlayers, generating now. +Installing Dependencies for openlayers +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building openlayers +$ parcel build src/script.js -d static --no-source-maps +npm WARN deprecated babel-preset-es2015@6.24.1: 🙌 Thanks for using Babel: we recommend using babel-preset-env now: please read https://babeljs.io/env to update! +npm WARN deprecated core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. +npm WARN lifecycle The node binary used for scripts is /tmp/yarn--1645049705295-0.7828872097284614/node but npm is using /home/me/.planemo/gx_venv_3/bin/node itself. Use the `--scripts-prepend-node-path` option to include the path for the node binary npm was executed with. + +> core-js@2.6.12 postinstall /tmp/tmp1upz926i/galaxy-dev/config/plugins/visualizations/openlayers/node_modules/wkt-parser/node_modules/core-js +> node -e "try{require('./postinstall')}catch(e){}" + +npm notice created a lockfile as package-lock.json. You should commit this file. ++ babel-preset-es2015@6.24.1 +added 66 packages from 14 contributors and audited 66 packages in 3.207s +found 0 vulnerabilities + +⚠️ Could not infer babel version. Defaulting to babel 7. Please add either babel-core or @babel/core as a dependency. ++ @babel/core@7.17.4 +added 52 packages from 62 contributors and audited 118 packages in 2.432s + +3 packages are looking for funding + run `npm fund` for details + +found 0 vulnerabilities + +✨ Built in 20.10s. + +static/script.js ⚠️ 1.33 MB 19.74s +No build hashfile detected for openseadragon, generating now. +Installing Dependencies for openseadragon +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building openseadragon +$ cpy --cwd='node_modules/openseadragon/build/openseadragon' --parents './' '../../../../static/dist' +No build hashfile detected for pv, generating now. +Installing Dependencies for pv +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building pv +$ parcel build src/pv.js -d static/dist +✨ Built in 3.78s. + +static/dist/pv.js.map 492.04 KB 44ms +static/dist/pv.js 160.92 KB 3.42s +No build hashfile detected for new_user, generating now. +Installing Dependencies for new_user +info No lockfile found. +[1/4] Resolving packages... +[2/4] Fetching packages... +[3/4] Linking dependencies... +[4/4] Building fresh packages... +success Saved lockfile. +Building new_user +$ webpack --mode production +Hash: e9be2ddae440d20be158 +Version: webpack 4.46.0 +Time: 379ms +Built at: 02/16/2022 5:15:51 PM + Asset Size Chunks Chunk Names + static/topics/README.md 1.52 KiB [emitted] + static/topics/data/images/data_importer/data_in_history.png 47.2 KiB [emitted] + static/topics/data/images/data_importer/ftp_button.png 9.52 KiB [emitted] + static/topics/data/images/data_importer/importer_button.png 12.7 KiB [emitted] + static/topics/data/images/data_importer/importer_icon.png 4.53 KiB [emitted] + static/topics/data/images/data_importer/importer_modal.png 110 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./src/onload/index.js + 13 modules 17.1 KiB {7} {8} {9} {10} [built] + | ./src/onload/index.js 916 bytes [built] + | ./src/onload/publicPath.js 540 bytes [built] + | ./src/onload/standardInit.js 4.08 KiB [built] + | ./src/onload/defaultAppFactory.js 679 bytes [built] + | ./src/onload/globalInits/index.js 1.22 KiB [built] + | ./src/utils/installMonitor.js 4.54 KiB [built] + | ./src/onload/globalInits/initSentry.js 722 bytes [built] + | ./src/onload/globalInits/initTooltips.js 494 bytes [built] + | ./src/onload/globalInits/iframesAreTerrible.js 1.11 KiB [built] + | ./src/onload/globalInits/onloadWebhooks.js 497 bytes [built] + | ./src/onload/globalInits/replace_big_select_inputs.js 1.57 KiB [built] + | ./src/onload/globalInits/initTours.js 182 bytes [built] + | ./src/onload/globalInits/initModals.js 225 bytes [built] + | ./src/utils/mock.js 348 bytes [built] + [525] ./src/layout/page.js 5.44 KiB {7} {8} {10} [built] + [547] ./src/polyfills.js 2.99 KiB {7} {8} {9} {10} [built] + [558] ./src/bundleEntries-exposed.js 457 bytes {7} {8} {9} {10} [built] + [619] ./src/bundleEntries.js + 217 modules 699 KiB {7} {8} {9} {10} [built] + | ./src/bundleEntries.js 4.13 KiB [built] + | ./src/viz/circster.js 36 KiB [built] + | ./src/layout/modal.js 3.97 KiB [built] + | ./src/viz/phyloviz.js 30.5 KiB [built] + | ./src/viz/sweepster.js 29.4 KiB [built] + | ./src/galaxy.library.js 6.68 KiB [built] + | ./src/mvc/history/multi-panel.js 41.6 KiB [built] + | ./src/mvc/history/history-view-annotated.js 3.85 KiB [built] + | ./src/legacy/grid/grid-view.js 20.2 KiB [built] + | ./src/reports/run_stats.js 16.2 KiB [built] + | ./src/toolshed/toolshed.groups.js 1.14 KiB [built] + | ./src/galaxy.interactive_environments.js 9.15 KiB [built] + | ./src/mvc/embedded-objects.js 2.65 KiB [built] + | ./src/utils/async-save-text.js 2.41 KiB [built] + | ./src/mvc/visualization/chart/chart-client.js 1.94 KiB [built] + | + 203 hidden modules +[1379] multi polyfills bundleEntries entry/login 52 bytes {10} [built] +[1860] multi polyfills bundleEntries entry/analysis 52 bytes {8} [built] +[2219] multi polyfills bundleEntries entry/admin 52 bytes {7} [built] +[2226] multi polyfills bundleEntries entry/generic 52 bytes {9} [built] +[2227] ./src/entry/generic.js 122 bytes {9} [built] +[2336] ./src/entry/analysis/index.js + 576 modules 924 KiB {8} [built] + | ./src/entry/analysis/index.js 1.18 KiB [built] + | ./src/entry/analysis/AnalysisRouter.js 20.1 KiB [built] + | ./src/entry/panels/tool-panel.js 1.11 KiB [built] + | ./src/entry/panels/history-panel.js 3.74 KiB [built] + | ./src/mvc/grid/grid-shared.js 2.2 KiB [built] + | ./src/mvc/history/history-list.js 4.25 KiB [built] + | ../static/plugins/welcome_page/new_user/dist/static/topics/index.js 289 bytes [built] + | ./src/mvc/history/options-menu.js 6.67 KiB [built] + | ./src/mvc/history/history-view-edit-current.js 18.5 KiB [built] + | ../static/plugins/welcome_page/new_user/dist/static/topics/scripts/combine.js 107 bytes [built] + | ./src/mvc/entrypoints/poll.js 823 bytes [built] + | ./src/utils/observable/whenAny.js 468 bytes [built] + | ./src/utils/math.js 103 bytes [built] + | ./src/utils/validation.js 542 bytes [built] + | ./src/utils/observable/index.js 897 bytes [built] + | + 562 hidden modules +[2337] ./src/entry/admin/index.js + 253 modules 272 KiB {7} [built] + | ./src/entry/admin/index.js 692 bytes [built] + | ./src/entry/admin/AdminRouter.js 7.85 KiB [built] + | ./src/entry/panels/admin-panel.js 5.03 KiB [built] + | + 251 hidden modules +[2338] ./src/entry/login/index.js + 15 modules 14.6 KiB {10} [built] + | ./src/entry/login/index.js 1.07 KiB [built] + | + 15 hidden modules + + 3072 hidden modules + +WARNING in ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& (./node_modules/babel-loader/lib??ref--2!./node_modules/vue-loader/lib??vue-loader-options!./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js&) 40:16-26 +"export 'JobMetrics' was not found in 'components/JobMetrics/JobMetrics' + @ ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& + @ ./src/components/JobInformation/JobDetails.vue + @ ./node_modules/babel-loader/lib??ref--2!./node_modules/vue-loader/lib??vue-loader-options!./src/components/admin/Jobs.vue?vue&type=script&lang=js& + @ ./src/components/admin/Jobs.vue?vue&type=script&lang=js& + @ ./src/components/admin/Jobs.vue + @ ./src/entry/admin/AdminRouter.js + @ ./src/entry/admin/index.js + @ multi polyfills bundleEntries entry/admin + +WARNING in ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& (./node_modules/babel-loader/lib??ref--2!./node_modules/vue-loader/lib??vue-loader-options!./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js&) 41:19-32 +"export 'JobParameters' was not found in 'components/JobParameters/JobParameters' + @ ./src/components/JobInformation/JobDetails.vue?vue&type=script&lang=js& + @ ./src/components/JobInformation/JobDetails.vue + @ ./node_modules/babel-loader/lib??ref--2!./node_modules/vue-loader/lib??vue-loader-options!./src/components/admin/Jobs.vue?vue&type=script&lang=js& + @ ./src/components/admin/Jobs.vue?vue&type=script&lang=js& + @ ./src/components/admin/Jobs.vue + @ ./src/entry/admin/AdminRouter.js + @ ./src/entry/admin/index.js + @ multi polyfills bundleEntries entry/admin + +WARNING in chunk base [mini-css-extract-plugin] +Conflicting order. Following module has been added: + * css ./node_modules/css-loader/dist/cjs.js??ref--8-1!./node_modules/vue-loader/lib/loaders/stylePostLoader.js!./node_modules/postcss-loader/src??ref--8-2!./node_modules/sass-loader/dist/cjs.js??ref--8-3!./node_modules/vue-loader/lib??vue-loader-options!./src/components/Collections/common/ClickToEdit.vue?vue&type=style&index=0&lang=css& +despite it was not able to fulfill desired ordering with these modules: + * css ./node_modules/css-loader/dist/cjs.js??ref--8-1!./node_modules/vue-loader/lib/loaders/stylePostLoader.js!./node_modules/postcss-loader/src??ref--8-2!./node_modules/sass-loader/dist/cjs.js??ref--8-3!./node_modules/vue-loader/lib??vue-loader-options!./src/components/Collections/UnpairedDatasetElementView.vue?vue&type=style&index=0&lang=css& + - couldn't fulfill desired order of chunk group(s) PairedListCollectionCreator + - while fulfilling desired order of chunk group(s) analysis + +WARNING in core-js + Multiple versions of core-js found: + 2.6.5 ./~/@babel/polyfill/~/core-js + 3.18.3 ./~/core-js + + +WARNING in es-abstract + Multiple versions of es-abstract found: + 1.17.7 ./~/regexp.prototype.flags/~/es-abstract + 1.18.0-next.1 ./~/es-abstract + + +WARNING in isarray + Multiple versions of isarray found: + 1.0.0 ./~/isarray + 2.0.5 ./~/deep-equal/~/isarray + + +WARNING in lodash + Multiple versions of lodash found: + 4.17.11 ./~/vueisotope/~/lodash + 4.17.20 ./~/lodash + + +WARNING in object-keys + Multiple versions of object-keys found: + 1.0.12 ./~/define-properties/~/object-keys + 1.1.1 ./~/object-keys + + +WARNING in tslib + Multiple versions of tslib found: + 1.13.0 ./~/tslib + 1.9.3 ./~/rxjs/~/tslib + +Check how you can resolve duplicate packages: +https://github.com/darrenscerri/duplicate-package-checker-webpack-plugin#resolving-duplicate-packages-in-your-bundle + + +WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB). +This can impact web performance. +Assets: + CacheWorker.worker.bundled.worker.js (943 KiB) + assets/3c45c98f6f6c1b009c082510d0255ef4.svg (699 KiB) + assets/18df003f90a7f1313b98b23384ec4f1b.svg (876 KiB) + libs.chunk.js (3.35 MiB) + base.css (2.89 MiB) + admin.bundled.js (2.26 MiB) + analysis.bundled.js (2.77 MiB) + generic.bundled.js (2.08 MiB) + login.bundled.js (2.11 MiB) + vendors~Screenshot.chunk.js (340 KiB) + vendors~ruleCollectionBuilder.chunk.js (621 KiB) + vendors~workflowLayout.chunk.js (1.27 MiB) + base.css.map (7.35 MiB) + +WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance. +Entrypoints: + login (8.34 MiB) + base.css + base.chunk.js + libs.chunk.js + login.bundled.js + analysis (9 MiB) + base.css + base.chunk.js + libs.chunk.js + analysis.bundled.js + admin (8.5 MiB) + base.css + base.chunk.js + libs.chunk.js + admin.bundled.js + generic (8.32 MiB) + base.css + base.chunk.js + libs.chunk.js + generic.bundled.js + +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/splitpanes/dist/splitpanes.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/vue-multiselect/dist/vue-multiselect.min.css: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!src/components/History/ContentItem/styles.scss: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!src/components/History/adapters/HistoryPanelProxy.scss: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!src/style/scss/base.scss: + Entrypoint mini-css-extract-plugin = * + [0] ./node_modules/css-loader/dist/cjs.js??ref--8-1!./node_modules/postcss-loader/src??ref--8-2!./node_modules/sass-loader/dist/cjs.js??ref--8-3!./src/style/scss/base.scss 2.92 MiB {0} [built] + [18] 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mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/handsontable/dist/handsontable.full.css?vue&type=style&index=0&lang=css&: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/vue-loader/lib/index.js??vue-loader-options!src/components/Citation/Citation.vue?vue&type=style&index=0&lang=css&: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin 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node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/vue-loader/lib/index.js??vue-loader-options!src/components/Collections/common/ClickToEdit.vue?vue&type=style&index=0&lang=css&: + Entrypoint mini-css-extract-plugin = * + 2 modules +Child mini-css-extract-plugin node_modules/css-loader/dist/cjs.js??ref--8-1!node_modules/vue-loader/lib/loaders/stylePostLoader.js!node_modules/postcss-loader/src/index.js??ref--8-2!node_modules/sass-loader/dist/cjs.js??ref--8-3!node_modules/vue-loader/lib/index.js??vue-loader-options!src/components/Collections/common/CollectionCreator.vue?vue&type=style&index=0&lang=scss&: + Entrypoint mini-css-extract-plugin = * + 13 modules +Child mini-css-extract-plugin 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2>/dev/null || echo '') >../static/client_build_hash.txt +Done in 372.09s. +/tmp/tmp1upz926i/galaxy-dev +Starting Galaxy with command [cd /tmp/tmp1upz926i/galaxy-dev && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /usr/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && /tmp/tmp1upz926i/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --server-name main] +Activated a virtualenv for Galaxy +/home/me/.planemo/gx_venv_3 +Set COMMON_STARTUP_ARGS to --dev-wheels +Activating virtualenv at /home/me/.planemo/gx_venv_3 +Requirement already satisfied: pip>=19.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (20.0.2) +Ignoring async-exit-stack: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring async-generator: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring atomicwrites: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring cached-property: markers 'python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring cffi: markers 'implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")' don't match your environment +Ignoring colorama: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0"' don't match your environment +Ignoring contextvars: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring dataclasses: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring immutables: markers 'python_version >= "3.6" and python_version < "3.7"' don't match your environment +Ignoring importlib-metadata: markers 'python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8")' don't match your environment +Ignoring importlib-resources: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Ignoring py: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.4.0" and python_version >= "3.6" and implementation_name == "pypy"' don't match your environment +Ignoring pycparser: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32" and python_version >= "3.8"' don't match your environment +Ignoring pyreadline: markers 'python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" and sys_platform == "win32" or python_version >= "3.6" and python_version < "3.8" and python_full_version >= "3.5.0" and sys_platform == "win32"' don't match your environment +Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"' don't match your environment +Ignoring typing-extensions: markers 'python_version >= "3.6" and python_version < "3.8"' don't match your environment +Ignoring zipp: markers 'python_version < "3.7" and python_version >= "3.6"' don't match your environment +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple +Requirement already satisfied: adal==1.2.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (1.2.7) +Requirement already satisfied: aiofiles==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.6.0) +Requirement already satisfied: alabaster==0.7.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (0.7.12) +Requirement already satisfied: amqp==5.0.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 6)) (5.0.6) +Requirement already satisfied: appdirs==1.4.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 7)) (1.4.4) +Requirement already satisfied: argcomplete==1.12.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (1.12.3) +Requirement already satisfied: attmap==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (0.13.0) +Requirement already satisfied: attrs==20.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (20.3.0) +Requirement already satisfied: babel==2.9.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (2.9.0) +Requirement already satisfied: bagit-profile==1.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 15)) (1.3.1) +Requirement already satisfied: bagit==1.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (1.8.1) +Requirement already satisfied: bcrypt==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (3.2.0) +Requirement already satisfied: bdbag==1.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (1.6.1) +Requirement already satisfied: beaker==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 19)) (1.11.0) +Requirement already satisfied: billiard==3.6.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (3.6.4.0) +Requirement already satisfied: bioblend==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (0.15.0) +Requirement already satisfied: bleach==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (3.3.0) +Requirement already satisfied: boltons==20.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 23)) (20.2.1) +Requirement already satisfied: boto3==1.16.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (1.16.63) +Requirement already satisfied: boto==2.49.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 25)) (2.49.0) +Requirement already satisfied: botocore==1.19.63 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 26)) (1.19.63) +Requirement already satisfied: bx-python==0.8.11 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.8.11) +Requirement already satisfied: cachecontrol==0.11.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.11.7) +Requirement already satisfied: cachetools==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (4.2.2) +Requirement already satisfied: celery==5.0.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 31)) (5.0.5) +Requirement already satisfied: certifi==2020.12.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (2020.12.5) +Requirement already satisfied: chardet==4.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (4.0.0) +Requirement already satisfied: cheetah3==3.2.6.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 35)) (3.2.6.post1) +Requirement already satisfied: circus==0.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 36)) (0.17.1) +Requirement already satisfied: click-didyoumean==0.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (0.0.3) +Requirement already satisfied: click-plugins==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.1.1) +Requirement already satisfied: click-repl==0.1.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (0.1.6) +Requirement already satisfied: click==7.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (7.1.2) +Requirement already satisfied: cliff==3.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (3.7.0) +Requirement already satisfied: cloudauthz==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.6.0) +Requirement already satisfied: cloudbridge==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (2.1.0) +Requirement already satisfied: cmd2==1.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (1.5.0) +Requirement already satisfied: coloredlogs==15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (15.0) +Requirement already satisfied: commonmark==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 47)) (0.9.1) +Requirement already satisfied: coverage==5.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (5.5) +Requirement already satisfied: cryptography==3.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 50)) (3.4.7) +Requirement already satisfied: cwltool==3.0.20201109103151 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (3.0.20201109103151) +Requirement already satisfied: debtcollector==2.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (2.2.0) +Requirement already satisfied: decorator==5.0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (5.0.7) +Requirement already satisfied: defusedxml==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (0.7.1) +Requirement already satisfied: deprecated==1.2.12 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.2.12) +Requirement already satisfied: deprecation==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (0.4) +Requirement already satisfied: docopt==0.6.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (0.6.2) +Requirement already satisfied: docutils==0.16 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (0.16) +Requirement already satisfied: dogpile.cache==1.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (1.1.2) +Requirement already satisfied: ecdsa==0.14.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (0.14.1) +Requirement already satisfied: edam-ontology==1.25.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 63)) (1.25.2) +Requirement already satisfied: fabric3==1.14.post1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (1.14.post1) +Requirement already satisfied: fastapi-utils==0.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 65)) (0.2.1) +Requirement already satisfied: fastapi==0.65.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 66)) (0.65.2) +Requirement already satisfied: fluent-logger==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (0.10.0) +Requirement already satisfied: fs==2.4.13 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 68)) (2.4.13) +Requirement already satisfied: funcsigs==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 69)) (1.0.2) +Requirement already satisfied: future==0.18.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 70)) (0.18.2) +Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 71)) (1.1.5) +Requirement already satisfied: google-api-core==1.26.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 72)) (1.26.3) +Requirement already satisfied: google-api-python-client==1.12.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 73)) (1.12.8) +Requirement already satisfied: google-auth-httplib2==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 74)) (0.1.0) +Requirement already satisfied: google-auth==1.30.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 75)) (1.30.0) +Requirement already satisfied: googleapis-common-protos==1.53.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 76)) (1.53.0) +Requirement already satisfied: greenlet==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 77)) (1.0.0) +Requirement already satisfied: gunicorn==20.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 78)) (20.1.0) +Requirement already satisfied: gxformat2==0.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 79)) (0.15.0) +Requirement already satisfied: h11==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 80)) (0.12.0) +Requirement already satisfied: h5py==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 81)) (3.1.0) +Requirement already satisfied: httpcore==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 82)) (0.13.0) +Requirement already satisfied: httplib2==0.19.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 83)) (0.19.1) +Requirement already satisfied: httpx==0.18.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 84)) (0.18.0) +Requirement already satisfied: humanfriendly==9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 85)) (9.1) +Requirement already satisfied: idna==2.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 86)) (2.10) +Requirement already satisfied: imagesize==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 87)) (1.2.0) +Requirement already satisfied: iniconfig==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 91)) (1.1.1) +Requirement already satisfied: isa-rwval==0.10.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 92)) (0.10.10) +Requirement already satisfied: iso8601==0.1.14 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 93)) (0.1.14) +Requirement already satisfied: isodate==0.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 94)) (0.6.0) +Requirement already satisfied: jinja2==2.11.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 95)) (2.11.3) +Requirement already satisfied: jmespath==0.10.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 96)) (0.10.0) +Requirement already satisfied: jsonpatch==1.32 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 97)) (1.32) +Requirement already satisfied: jsonpointer==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 98)) (2.1) +Requirement already satisfied: jsonschema==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 99)) (3.2.0) +Requirement already satisfied: keystoneauth1==4.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 100)) (4.3.1) +Requirement already satisfied: kombu==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 101)) (5.0.2) +Requirement already satisfied: lagom==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 102)) (1.2.0) +Requirement already satisfied: lockfile==0.12.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 103)) (0.12.2) +Requirement already satisfied: lxml==4.6.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 104)) (4.6.3) +Requirement already satisfied: mako==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 105)) (1.1.4) +Requirement already satisfied: markdown-it-reporter==0.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 106)) (0.0.2) +Requirement already satisfied: markdown==3.3.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 107)) (3.3.4) +Requirement already satisfied: markupsafe==1.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 108)) (1.1.1) +Requirement already satisfied: mercurial==5.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 109)) (5.7.1) +Requirement already satisfied: mirakuru==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 110)) (2.3.0) +Requirement already satisfied: mistune==0.8.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 111)) (0.8.4) +Requirement already satisfied: mrcfile==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 112)) (1.3.0) +Requirement already satisfied: msgpack==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 113)) (1.0.2) +Requirement already satisfied: munch==2.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 114)) (2.5.0) +Requirement already satisfied: mypy-extensions==0.4.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 115)) (0.4.3) +Requirement already satisfied: netaddr==0.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 116)) (0.8.0) +Requirement already satisfied: netifaces==0.10.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 117)) (0.10.9) +Requirement already satisfied: networkx==2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 118)) (2.5) +Requirement already satisfied: nodeenv==1.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 119)) (1.6.0) +Requirement already satisfied: nose==1.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 120)) (1.3.7) +Requirement already satisfied: nosehtml==0.4.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 121)) (0.4.6) +Requirement already satisfied: numpy==1.19.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 122)) (1.19.5) +Requirement already satisfied: oauth2client==4.1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 123)) (4.1.3) +Requirement already satisfied: oauthlib==3.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 124)) (3.1.0) +Requirement already satisfied: openstacksdk==0.52.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 125)) (0.52.0) +Requirement already satisfied: os-client-config==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 126)) (2.1.0) +Requirement already satisfied: os-service-types==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 127)) (1.7.0) +Requirement already satisfied: osc-lib==2.3.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 128)) (2.3.1) +Requirement already satisfied: oslo.config==8.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 129)) (8.6.0) +Requirement already satisfied: oslo.context==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 130)) (3.2.0) +Requirement already satisfied: oslo.i18n==5.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 131)) (5.0.1) +Requirement already satisfied: oslo.log==4.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 132)) (4.4.0) +Requirement already satisfied: oslo.serialization==4.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 133)) (4.1.0) +Requirement already satisfied: oslo.utils==4.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 134)) (4.8.0) +Requirement already satisfied: oyaml==1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 135)) (1.0) +Requirement already satisfied: packaging==20.9 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 136)) (20.9) +Requirement already satisfied: paramiko==2.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 137)) (2.7.2) +Requirement already satisfied: parsley==1.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 138)) (1.3) +Requirement already satisfied: paste==3.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 139)) (3.5.0) +Requirement already satisfied: pastedeploy==2.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 140)) (2.1.1) +Requirement already satisfied: pbr==5.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 141)) (5.6.0) +Requirement already satisfied: pluggy==0.13.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 142)) (0.13.1) +Requirement already satisfied: port-for==0.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 143)) (0.4) +Requirement already satisfied: prettytable==0.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 144)) (0.7.2) +Requirement already satisfied: prompt-toolkit==3.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 145)) (3.0.3) +Requirement already satisfied: protobuf==3.15.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 146)) (3.15.8) +Requirement already satisfied: prov==1.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 147)) (1.5.1) +Requirement already satisfied: psutil==5.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 148)) (5.8.0) +Requirement already satisfied: pulsar-galaxy-lib==0.14.10 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 149)) (0.14.10) +Requirement already satisfied: pyasn1-modules==0.2.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 151)) (0.2.8) +Requirement already satisfied: pyasn1==0.4.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 152)) (0.4.8) +Requirement already satisfied: pycryptodome==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 154)) (3.10.1) +Requirement already satisfied: pydantic==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 155)) (1.8.2) +Requirement already satisfied: pydot==1.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 156)) (1.4.2) +Requirement already satisfied: pyeventsystem==0.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 157)) (0.1.0) +Requirement already satisfied: pyfaidx==0.5.9.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 158)) (0.5.9.5) +Requirement already satisfied: pygithub==1.55 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 159)) (1.55) +Requirement already satisfied: pygments==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 160)) (2.8.1) +Requirement already satisfied: pyinotify==0.9.6 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 161)) (0.9.6) +Requirement already satisfied: pyjwt==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 162)) (2.1.0) +Requirement already satisfied: pykwalify==1.8.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 163)) (1.8.0) +Requirement already satisfied: pynacl==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 164)) (1.4.0) +Requirement already satisfied: pyparsing==2.4.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 165)) (2.4.7) +Requirement already satisfied: pyperclip==1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 166)) (1.8.2) +Requirement already satisfied: pyrsistent==0.17.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 169)) (0.17.3) +Requirement already satisfied: pysam==0.16.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 170)) (0.16.0.1) +Requirement already satisfied: pytest-asyncio==0.15.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 171)) (0.15.1) +Requirement already satisfied: pytest-cov==2.11.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 172)) (2.11.1) +Requirement already satisfied: pytest-html==3.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 173)) (3.1.1) +Requirement already satisfied: pytest-json-report==1.2.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 174)) (1.2.4) +Requirement already satisfied: pytest-metadata==1.11.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 175)) (1.11.0) +Requirement already satisfied: pytest-mock==3.6.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 176)) (3.6.0) +Requirement already satisfied: pytest-postgresql==2.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 177)) (2.6.1) +Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 178)) (0.7.3) +Requirement already satisfied: pytest-shard==0.1.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 179)) (0.1.2) +Requirement already satisfied: pytest==6.2.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (6.2.3) +Requirement already satisfied: python-dateutil==2.8.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 181)) (2.8.1) +Requirement already satisfied: python-irodsclient==1.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 182)) (1.0.0) +Requirement already satisfied: python-jose==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 183)) (3.2.0) +Requirement already satisfied: python-keystoneclient==4.1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 184)) (4.1.1) +Requirement already satisfied: python-neutronclient==7.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 185)) (7.2.1) +Requirement already satisfied: python-novaclient==17.2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 186)) (17.2.1) +Requirement already satisfied: python-swiftclient==3.10.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 187)) (3.10.1) +Requirement already satisfied: python3-openid==3.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 188)) (3.2.0) +Requirement already satisfied: pytz==2021.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 189)) (2021.1) +Requirement already satisfied: pyuwsgi==2.0.19.1.post0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 190)) (2.0.19.1.post0) +Requirement already satisfied: pyyaml==5.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 191)) (5.4.1) +Requirement already satisfied: pyzmq==22.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 192)) (22.0.3) +Requirement already satisfied: rdflib-jsonld==0.5.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 193)) (0.5.0) +Requirement already satisfied: rdflib==4.2.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 194)) (4.2.2) +Requirement already satisfied: recommonmark==0.7.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 195)) (0.7.1) +Requirement already satisfied: refgenconf==0.12.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (0.12.0) +Requirement already satisfied: repoze.lru==0.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 197)) (0.7) +Requirement already satisfied: requests-oauthlib==1.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 198)) (1.3.0) +Requirement already satisfied: requests-toolbelt==0.9.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 199)) (0.9.1) +Requirement already satisfied: requests==2.25.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 200)) (2.25.1) +Requirement already satisfied: requestsexceptions==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 201)) (1.4.0) +Requirement already satisfied: responses==0.13.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 202)) (0.13.3) +Requirement already satisfied: rfc3986==1.4.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 203)) (1.4.0) +Requirement already satisfied: routes==2.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 204)) (2.5.1) +Requirement already satisfied: rsa==4.7.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 205)) (4.7.2) +Requirement already satisfied: ruamel.yaml==0.16.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 207)) (0.16.5) +Requirement already satisfied: s3transfer==0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 208)) (0.3.7) +Requirement already satisfied: schema-salad==7.1.20210316164414 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 209)) (7.1.20210316164414) +Requirement already satisfied: selenium==3.141.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 210)) (3.141.0) +Requirement already satisfied: setuptools-scm==5.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 211)) (5.0.2) +Requirement already satisfied: shellescape==3.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 212)) (3.4.1) +Requirement already satisfied: simplejson==3.17.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 213)) (3.17.2) +Requirement already satisfied: six==1.15.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 214)) (1.15.0) +Requirement already satisfied: sniffio==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 215)) (1.2.0) +Requirement already satisfied: snowballstemmer==2.1.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 216)) (2.1.0) +Requirement already satisfied: social-auth-core==4.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 217)) (4.0.3) +Requirement already satisfied: sortedcontainers==2.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 218)) (2.3.0) +Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 219)) (0.0.15) +Requirement already satisfied: sphinx-rtd-theme==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 220)) (0.5.2) +Requirement already satisfied: sphinx==3.5.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 221)) (3.5.4) +Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 222)) (1.0.2) +Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 223)) (1.0.2) +Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 224)) (1.0.3) +Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 225)) (1.0.1) +Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 226)) (1.0.3) +Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 227)) (1.1.4) +Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 228)) (0.13.0) +Requirement already satisfied: sqlalchemy==1.4.20 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 229)) (1.4.20) +Requirement already satisfied: sqlitedict==1.7.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 230)) (1.7.0) +Requirement already satisfied: sqlparse==0.4.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 231)) (0.4.2) +Requirement already satisfied: starlette-context==0.3.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 232)) (0.3.2) +Requirement already satisfied: starlette==0.14.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 233)) (0.14.2) +Requirement already satisfied: statsd==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 234)) (3.3.0) +Requirement already satisfied: stevedore==3.3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 235)) (3.3.0) +Requirement already satisfied: svgwrite==1.4.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 236)) (1.4.1) +Requirement already satisfied: tempita==0.5.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 237)) (0.5.2) +Requirement already satisfied: tenacity==7.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 238)) (7.0.0) +Requirement already satisfied: testfixtures==6.17.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 239)) (6.17.1) +Requirement already satisfied: tifffile==2020.9.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 240)) (2020.9.3) +Requirement already satisfied: toml==0.10.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 241)) (0.10.2) +Requirement already satisfied: tornado==6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 242)) (6.1) +Requirement already satisfied: tqdm==4.60.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 243)) (4.60.0) +Requirement already satisfied: twill==3.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 244)) (3.0) +Requirement already satisfied: tzlocal==2.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 246)) (2.1) +Requirement already satisfied: ubiquerg==0.6.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 247)) (0.6.1) +Requirement already satisfied: unidecode==1.2.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 248)) (1.2.0) +Requirement already satisfied: uritemplate==3.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 249)) (3.0.1) +Requirement already satisfied: urllib3==1.26.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 250)) (1.26.4) +Requirement already satisfied: uvicorn==0.13.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 251)) (0.13.4) +Requirement already satisfied: vine==5.0.0 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 252)) (5.0.0) +Requirement already satisfied: watchdog==2.0.3 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 253)) (2.0.3) +Requirement already satisfied: wcwidth==0.2.5 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 254)) (0.2.5) +Requirement already satisfied: webencodings==0.5.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 255)) (0.5.1) +Requirement already satisfied: webob==1.8.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 256)) (1.8.7) +Requirement already satisfied: whoosh==2.7.4 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 257)) (2.7.4) +Requirement already satisfied: wrapt==1.12.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 258)) (1.12.1) +Requirement already satisfied: xmlrunner==1.7.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 259)) (1.7.7) +Requirement already satisfied: yacman==0.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 260)) (0.8.2) +Requirement already satisfied: zipstream-new==1.1.8 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 262)) (1.1.8) +Requirement already satisfied: cffi>=1.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (1.15.0) +Requirement already satisfied: colorama>=0.3.7 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cmd2==1.5.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.4.4) +Requirement already satisfied: typing-extensions in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (4.1.1) +Requirement already satisfied: setuptools in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==3.0.20201109103151->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (44.0.0) +Requirement already satisfied: py>=1.8.2 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from pytest==6.2.3->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 180)) (1.11.0) +Requirement already satisfied: rich>=9.0.1 in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from refgenconf==0.12.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 196)) (11.2.0) +Requirement already satisfied: pycparser in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from cffi>=1.1->bcrypt==3.2.0->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (2.21) +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Requirement already satisfied: watchdog in /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r /dev/stdin (line 1)) (2.0.3) +The Galaxy client build is up to date and will not be rebuilt at this time. +Activating virtualenv at /home/me/.planemo/gx_venv_3 +Executing: gunicorn --pythonpath lib --paste "/tmp/tmp1upz926i/galaxy.ini"
--- a/precheck.xml Fri Jun 01 17:55:23 2018 -0400 +++ b/precheck.xml Wed Feb 16 22:59:00 2022 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="precheck" name="Du Novo: Check input" version="2.15"> +<tool id="precheck" name="Du Novo: Check input" version="3.0.2"> <requirements> - <requirement type="package" version="2.15">dunovo</requirement> + <requirement type="package" version="3.0.2">dunovo</requirement> </requirements> <description>for family content</description> <command detect_errors="exit_code">
--- a/tool_dependencies.xml Fri Jun 01 17:55:23 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bowtie" version="1.1.2"> - <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="mafft" version="7.221"> - <repository changeset_revision="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="networkx" version="1.10"> - <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="dunovo" version="2.15"> - <install version="1.0"> - <actions> - <!-- download the main dunovo package files --> - <action sha256sum="1cf02bcc37cc641a20bdf5e20c2b3b98d4dccd43b1182830cb1a9e7d173d1a78" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.15.tar.gz</action> - <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. --> - <!-- install submodules --> - <action type="shell_command">rmdir kalign utillib ET</action> - <!-- download the utillib submodule --> - <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action> - <action type="shell_command">rm v0.1.0.tar.gz</action> - <action rename_to="utillib" type="move_file"> - <source>utillib-0.1.0</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- download the kalign submodule --> - <action type="download_file">https://github.com/makovalab-psu/kalign-dunovo/archive/v0.2.0.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> - <action type="shell_command">rm v0.2.0.tar.gz</action> - <action rename_to="kalign" type="move_file"> - <source>kalign-dunovo-0.2.0</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- download the ET submodule --> - <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action> - <action type="shell_command">rm v0.2.2.tar.gz</action> - <action rename_to="ET" type="move_file"> - <source>ET-0.2.2</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- download the bfx submodule --> - <action type="download_file">https://github.com/NickSto/bfx/archive/v0.2.0.tar.gz</action> - <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> - <action type="shell_command">rm v0.2.0.tar.gz</action> - <action rename_to="bfx" type="move_file"> - <source>bfx-0.2.0</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- Move some source files from subdirectories into the main source directory. --> - <action type="move_file"> - <source>utils/precheck.py</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <action type="move_file"> - <source>bfx/trimmer.py</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <action type="move_file"> - <source>utils/getreads.py</source> - <destination>$TMP_WORK_DIR/dunovo-2.15</destination> - </action> - <!-- make and install --> - <action type="shell_command">make clean</action> - <action type="shell_command">make</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - </package> -</tool_dependency>