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changeset 13:09c1934e0c45 draft

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Uploaded
author petrn
date Thu, 02 Jan 2020 14:13:10 +0000
parents b4195377038d
children ac3abb440e3f
files repex_full_clustering.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/repex_full_clustering.xml	Thu Jan 02 14:12:13 2020 +0000
+++ b/repex_full_clustering.xml	Thu Jan 02 14:13:10 2020 +0000
@@ -10,7 +10,7 @@
    <requirements>
      <requirement type="package" version="3.7">python</requirement>
      <requirement type="package" version="0.9.1" >pyrserve</requirement>
-     <requirement type="package">last</requirement>
+     <requirement type="package" version="1021" >last</requirement>
      <requirement type="package">mafft</requirement>
      <requirement type="package">imagemagick</requirement>
      <requirement type="package">blast</requirement>
@@ -32,11 +32,11 @@
      <requirement type="package">r-rsqlite</requirement>
      <requirement type="package">r-rserve</requirement>
      <requirement type="package">bioconductor-biostrings</requirement>
+     <requirement type="set_environment">REPEX</requirement>
    </requirements>
     <command >
-      make -C ${__tool_directory__};
       export PYTHONHASHSEED=0;
-      ${__tool_directory__}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
+      \${REPEX}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${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