Mercurial > repos > jpayne > snp_pipeline

diff 6_merge_vcfs.xml @ 27:1044c9a132c5

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 13:24:56 -0500
parents 05f2f9e58b3f
children 1d77f9fb51f3
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--- a/6_merge_vcfs.xml	Wed Jan 31 13:23:51 2018 -0500
+++ b/6_merge_vcfs.xml	Wed Jan 31 13:24:56 2018 -0500
@@ -8,9 +8,9 @@
         <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:\$CONDA_DEFAULT/lib" &&
+        export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:\$CONDA_DEFAULT_ENV/lib" &&
         env &&
-        ls -lah \$CONDA_DEFAULT &&
+        ls -lah \$CONDA_DEFAULT_ENV &&
         python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
             #for $vcf in $vcfs
                 -n $vcf.element_identifier -f $vcf