comparison repex_full_clustering.xml @ 4:72c028e3e70e draft

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3:d1f67a13b70f

<tool id="repeatexplorer2_dev" 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" />
      <regex match="error" source="stderr" level="fatal" description="Unknown error" />
      <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
      <exit_code range="1:" level="fatal" description="Error" />
    </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>
   </requirements>
    <command >
      export PYTHONHASHSEED=0;
      \${REPEX}/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
      --assembly_min $advanced_options.assembly_min_cluster_size

      ${FastaFile}  >stdout.log 2> stderr.log ;
      echo "STDOUT CONTENT:" >> ${log} ;
      cat stdout.log >> ${log} ;
      echo "STDERR CONTENT:" >> ${log};
      cat stderr.log >> ${log} &&
      \${REPEX}/stderr_filter.py stderr.log &&
      cd tarean_output &&
      zip -r  ${ReportArchive}.zip * &&
      mv ${ReportArchive}.zip ${ReportArchive} &&
      cp index.html ${ReportFile} &&
      mkdir ${ReportFile.files_path} &&

4:72c028e3e70e

<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" />
      <regex match="error" source="stderr" level="fatal" description="Unknown error" />
      <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
      <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description>
   <requirements>
     <container type="singularity">shub://repeatexplorer/repex_tarean:0.3.8.dbaa07f</container>
   </requirements>
<command>
      export PYTHONHASHSEED=0;
      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
      --assembly_min $advanced_options.assembly_min_cluster_size

      ${FastaFile}  >stdout.log 2> stderr.log ;
      echo "STDOUT CONTENT:" >> ${log} ;
      cat stdout.log >> ${log} ;
      echo "STDERR CONTENT:" >> ${log};
      cat stderr.log >> ${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} &&