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diff bwa.xml @ 12:086ba7b646e5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:35:56 -0400
parents 6def3ba376a7
children 22b497739c9c
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line diff
--- a/bwa.xml	Tue Apr 10 18:40:10 2018 -0400
+++ b/bwa.xml	Thu Sep 05 19:35:56 2019 -0400
@@ -209,7 +209,7 @@
   '${reference_fasta_filename}' first.sai '${input_type.bam_input}'
 #end if
 
-| samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output'
+| samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
 ]]>
     </command>