Mercurial > repos > devteam > bowtie2

diff bowtie2_wrapper.xml @ 26:1fc8d53bc352 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:35:26 -0400
parents 739b008acace
children c9105910063f
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--- a/bowtie2_wrapper.xml	Fri Aug 23 13:24:01 2019 -0400
+++ b/bowtie2_wrapper.xml	Thu Sep 05 19:35:26 2019 -0400
@@ -305,7 +305,7 @@
 
 ## output file
 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
-    | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
+    | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
 #else if $sam_options.reorder:
     | samtools view -bS - -o '$output'
 #else: