Mercurial > repos > petr-novak > repeatexplorer2
diff repex_tarean.xml @ 7:65d1a27e9339 draft default tip
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
| author | petr-novak |
|---|---|
| date | Mon, 16 Oct 2023 09:19:52 +0000 |
| parents | 335d138b654b |
| children |
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--- a/repex_tarean.xml Fri May 27 12:00:40 2022 +0000 +++ b/repex_tarean.xml Mon Oct 16 09:19:52 2023 +0000 @@ -6,36 +6,12 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> <description>Identification of genomic tandem repeats from NGS data</description> - <requirements> - <requirement type="package">imagemagick</requirement> - <requirement type="package">mafft</requirement> - <requirement type="package">blast</requirement> - <requirement type="package" version="0.9.29">diamond</requirement> - <requirement type="package">blast-legacy</requirement> - <requirement type="package">r-igraph</requirement> - <requirement type="package">r-data.tree</requirement> - <requirement type="package">r-stringr</requirement> - <requirement type="package">r-r2html</requirement> - <requirement type="package">r-hwriter</requirement> - <requirement type="package">r-dt</requirement> - <requirement type="package">r-scales</requirement> - <requirement type="package">r-plotrix</requirement> - <requirement type="package">r-png</requirement> - <requirement type="package">r-plyr</requirement> - <requirement type="package">r-dplyr</requirement> - <requirement type="package">r-optparse</requirement> - <requirement type="package">r-dbi</requirement> - <requirement type="package">r-rsqlite</requirement> - <requirement type="package">r-rserve</requirement> - <requirement type="package">bioconductor-biostrings</requirement> - <requirement type="package" version="2.3.8.1">repex_tarean</requirement> - <requirement type="set_environment">REPEX</requirement> - <requirement type="set_environment">REPEX_VERSION</requirement> - <requirement type="package" version="0.9.1">pyrserve</requirement> - </requirements> + <requirements> + <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container> + </requirements> <command detect_errors="exit_code"> export PYTHONHASHSEED=0; - \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode + seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode #if $advanced_options.advanced: --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging #if $advanced_options.custom_library.options_custom_library : @@ -53,21 +29,21 @@ cat stdout.log >> ${log} ; echo "STDERR CONTENT:" >> ${log} ; cat stderr.log >> ${log} && - \${REPEX}/stderr_filter.py stderr.log && + /opt/repex_tarean/stderr_filter.py stderr.log && cd tarean_output && zip -r ${ReportArchive}.zip * && mv ${ReportArchive}.zip ${ReportArchive} && cp index.html ${ReportFile} && - mkdir ${ReportFile.files_path} && - cp -r --parents libdir ${ReportFile.files_path} && - cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} && - cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} && - cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls && - cp *.png ${ReportFile.files_path}/ && - cp *.csv ${ReportFile.files_path}/ && - cp *.html ${ReportFile.files_path}/ && - cp *.css ${ReportFile.files_path}/ && - cp *.fasta ${ReportFile.files_path}/ 2>>$log && rm -r ../tarean_output || : + mkdir -p ${ReportFile.extra_files_path} && + cp -r --parents libdir ${ReportFile.extra_files_path} && + cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} && + cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} && + cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls && + cp *.png ${ReportFile.extra_files_path}/ && + cp *.csv ${ReportFile.extra_files_path}/ && + cp *.html ${ReportFile.extra_files_path}/ && + cp *.css ${ReportFile.extra_files_path}/ && + cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log && rm -r ../tarean_output || : </command> @@ -121,7 +97,28 @@ </when> </conditional> - + <conditional name="queue_definition"> + <param name="queue_select" type="select" label="Select queue"> + <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option> + <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option> + <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option> + </param> + <when value="basic_fast_queue"> + <param name="queue_specification" type="text" label="Modify parameters (optional)" + value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" /> + </when> + + <when value="long_slow_queue"> + <param name="queue_specification" type="text" label="Modify parameters (optional)" + value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" /> + </when> + <when value="extra_long_slow_queue"> + <param name="queue_specification" type="text" label="Modify parameters (optional)" + value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" /> + </when> + </conditional> + + </inputs> <outputs>