Mercurial > repos > iuc > samtools_markdup

diff samtools_markdup.xml @ 1:ec047bd60076 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:32:06 -0400
parents 57934f2719d8
children ba5470b53602
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--- a/samtools_markdup.xml	Fri Sep 28 04:28:25 2018 -0400
+++ b/samtools_markdup.xml	Thu Sep 05 19:32:06 2019 -0400
@@ -11,7 +11,7 @@
 ## coordinate sort input 
 #if not $bamfile.is_of_type('bam'):
     samtools sort
-    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
     -O sam
     -o coordsort.sam
     '$bamfile' &&