Mercurial > repos > petr-novak > repeatexplorer2_testing
diff repex_full_clustering.xml @ 4:72c028e3e70e draft
Uploaded
author | petr-novak |
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date | Thu, 08 Apr 2021 10:31:53 +0000 |
parents | d1f67a13b70f |
children | 397394c00bf7 |
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--- a/repex_full_clustering.xml Fri Jul 24 07:32:09 2020 -0400 +++ b/repex_full_clustering.xml Thu Apr 08 10:31:53 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="repeatexplorer2_dev" name="RepeatExplorer2 clustering: " version="2.3.8" > +<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8" > <stdio> <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" /> <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> @@ -8,40 +8,11 @@ </stdio> <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description> <requirements> - <requirement type="package" version="1.18.1">numpy</requirement> - <requirement type="package" version="0.8">logomaker</requirement> - <requirement type="package" version="1.0.3">pandas</requirement> - <requirement type="package" version="3.1.3">matplotlib</requirement> - <requirement type="package">last</requirement> - <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">repex_tarean_dev</requirement> - <requirement type="set_environment">REPEX</requirement> - <requirement type="set_environment">REPEX_VERSION</requirement> - <requirement type="package" version="0.9.1" >pyrserve</requirement> + <container type="singularity">shub://repeatexplorer/repex_tarean:0.3.8.dbaa07f</container> </requirements> - <command > +<command> export PYTHONHASHSEED=0; - \${REPEX}/seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon + seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon #if $advanced_options.advanced: --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx @@ -64,7 +35,7 @@ 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} &&