Mercurial > repos > iuc > samtools_merge

changeset 1:a27cd1e0d9a5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:32:34 -0400
parents ce3f4ecc9258
children 09015d802fdf
files samtools_merge.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_merge.xml	Fri Sep 28 04:24:35 2018 -0400
+++ b/samtools_merge.xml	Thu Sep 05 19:32:34 2019 -0400
@@ -15,7 +15,7 @@
 #for $i, $bam in enumerate( $bamfiles ):
     #if $bam.is_of_type('sam', 'cram', ):
         samtools sort
-        -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+        -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
         -O sam
         -o ${i}.sam
         '$bam' &&