Mercurial > repos > jpayne > snp_pipeline

diff 6_merge_vcfs.xml @ 20:baf9ccfae6f0

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 12:45:53 -0500
parents 4bb7e4a360bc
children 46b274d082a9
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--- a/6_merge_vcfs.xml	Wed Jan 31 12:38:03 2018 -0500
+++ b/6_merge_vcfs.xml	Wed Jan 31 12:45:53 2018 -0500
@@ -8,6 +8,12 @@
         <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        env &&
+        which bcftools &&
+        which bunzip    &&
+        which snp-pipeline &&
+        which python   &&
+        ldconfig -p | grep "libbz2.so*" &&
         python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
             #for $vcf in $vcfs
                 -n $vcf.element_identifier -f $vcf