Mercurial > repos > iuc > bwameth

diff bwameth.xml @ 5:4895589b7dab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:36:22 -0400
parents 06e882075239
children 368c79aa228f
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--- a/bwameth.xml	Wed Nov 08 13:16:44 2017 -0500
+++ b/bwameth.xml	Thu Sep 05 19:36:22 2019 -0400
@@ -78,7 +78,7 @@
     #else:
         $read1 $read2
     #end if
-    | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
+    | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
 ]]>
     </command>
     <inputs>