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diff bwa.xml @ 23:3fe632431b68 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 777181bd04849dab271ee2cc95e45c182947d308"
author iuc
date Tue, 19 May 2020 11:29:11 -0400
parents 8d2a528a9513
children e188dc7a68e6
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line diff
--- a/bwa.xml	Wed May 08 13:00:39 2019 -0400
+++ b/bwa.xml	Tue May 19 11:29:11 2020 -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>