diff repex_tarean.xml @ 4:72c028e3e70e draft

Uploaded

--- a/repex_tarean.xml	Fri Jul 24 07:32:09 2020 -0400
+++ b/repex_tarean.xml	Thu Apr 08 10:31:53 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="tarean_dev" name="Tandem Repeat Analyzer"  version="2.3.8" >
+<tool id="tarean" name="Tandem Repeat Analyzer"  version="2.3.8" >
     <stdio>
       <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
       <regex match="error" source="stderr" level="fatal" description="Unknown error" />
@@ -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">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>
+   <requirements>
+     <container type="singularity">shub://repeatexplorer/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 :
@@ -53,7 +29,7 @@
     cat stdout.log >> ${log} ;
     echo "STDERR CONTENT:" >> ${log} ;
     cat stderr.log >> ${log} &amp;&amp;
-    \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
+    /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
     cd tarean_output &amp;&amp;
     zip -r  ${ReportArchive}.zip * &amp;&amp;
     mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;