Mercurial > repos > petr-novak > repeatexplorer2_testing

changeset 4:72c028e3e70e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author petr-novak
date Thu, 08 Apr 2021 10:31:53 +0000
parents d1f67a13b70f
children 397394c00bf7
files repex_full_clustering.xml repex_tarean.xml tool_dependencies.xml
diffstat 3 files changed, 11 insertions(+), 73 deletions(-) [+]
line wrap: on
line diff
--- 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} &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;
--- 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;
--- a/tool_dependencies.xml	Fri Jul 24 07:32:09 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0" ?>
-<tool_dependency>
-    <package name="repex_tarean_dev" version="2.3.8">
-        <repository changeset_revision="0bccba287857" name="package_repex_tarean_2_3_8" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
-        <readme>
-      prepare repex database and scripts
-    </readme>
-    </package>
-</tool_dependency>
\ No newline at end of file