Mercurial > repos > iuc > samtools_fastx

diff samtools_fastx.xml @ 2:af994f4458bc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:31:10 -0400
parents a5429e2e18e8
children c933a9166b1d
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line diff
--- a/samtools_fastx.xml	Fri Sep 28 04:38:55 2018 -0400
+++ b/samtools_fastx.xml	Thu Sep 05 19:31:10 2019 -0400
@@ -10,7 +10,7 @@
 @ADDTHREADS@ 
 ## name sort input file if neccessary
 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
-    samtools sort -@ \$addthreads -n '$input' > input &&
+    samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
 #else:
     ln -s '$input' input &&
 #end if