Mercurial > repos > iuc > featurecounts

changeset 24:dfa29fefb36a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:36:53 -0400
parents 944deba3eb6a
children 9f24599f93e5
files featurecounts.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/featurecounts.xml	Thu Jun 06 17:53:42 2019 -0400
+++ b/featurecounts.xml	Thu Sep 05 19:36:53 2019 -0400
@@ -113,7 +113,7 @@
         #end if
 
         #if $extended_parameters.R:
-            && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam
+            && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
         #end if
         && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
     ]]></command>