Mercurial > repos > drosofff > msp_sr_bowtie

diff sRbowtie.py @ 7:5d82f9b15957 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Tue, 23 Jun 2015 16:59:01 -0400
parents d123b6e6a633
children a0bde9b84ca6
line wrap: on
line diff
--- a/sRbowtie.py	Thu Jun 11 09:22:04 2015 -0400
+++ b/sRbowtie.py	Tue Jun 23 16:59:01 2015 -0400
@@ -145,7 +145,7 @@
         # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam -
         # generates an "unsorted.bam.sorted.bam file", NOT an
         # "unsorted.bam.sorted" file
-        second_command_line = "/usr/bin/env samtools sort  %s %s" % (
+        second_command_line = "samtools sort  %s %s" % (
             path_to_unsortedBam, path_to_sortedBam)
         # fileno() method return the file descriptor number of tmp_stderr
         p = subprocess.Popen(