Mercurial > repos > iuc > bedtools

diff bamToBed.xml @ 51:b4cf5fca8773 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:34:55 -0400
parents df28283b3778
children 678ea22d643d
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line diff
--- a/bamToBed.xml	Mon Apr 29 05:54:22 2019 -0400
+++ b/bamToBed.xml	Thu Sep 05 19:34:55 2019 -0400
@@ -9,7 +9,7 @@
     <expand macro="stdio" />
     <command><![CDATA[
 #if $input.extension == 'bam' and $option == "-bedpe":
-    samtools sort -n '${input}' ./input &&
+    samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input &&
 #else
     ln -s '${input}' ./input.bam &&
 #end if