Mercurial > repos > iuc > bedtools

diff bamToBed.xml @ 35:b28e0cfa7ba1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author iuc
date Fri, 06 Sep 2019 14:29:59 -0400
parents dde39ba9c031
children fe5b4cb8356c
line wrap: on
line diff
--- a/bamToBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/bamToBed.xml	Fri Sep 06 14:29:59 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