--- a/repex_full_clustering.xml	Mon Jan 06 03:57:19 2020 -0500
+++ b/repex_full_clustering.xml	Mon Jan 06 03:59:39 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " >
+<tool id="repeatexplorer2x" name="RepeatExplorer2 clustering: " version="2.3.6" >
     <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" />
@@ -10,6 +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">mafft</requirement>
      <requirement type="package">imagemagick</requirement>
      <requirement type="package">blast</requirement>
@@ -31,10 +32,12 @@
      <requirement type="package">r-rsqlite</requirement>
      <requirement type="package">r-rserve</requirement>
      <requirement type="package">bioconductor-biostrings</requirement>
+     <requirement type="package" version="1.0">repex_tarean</requirement>
+     <requirement type="set_environment">REPEX</requirement>
    </requirements>
     <command >
       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