Mercurial > repos > drosofff > msp_sr_bowtie

changeset 5:d123b6e6a633 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author mvdbeek
date Thu, 11 Jun 2015 09:07:35 -0400
parents 0975f2267809
children 738a39851eae
files sRbowtie.py
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/sRbowtie.py	Thu Jun 11 08:54:56 2015 -0400
+++ b/sRbowtie.py	Thu Jun 11 09:07:35 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 = "samtools sort  %s %s" % (
+        second_command_line = "/usr/bin/env samtools sort  %s %s" % (
             path_to_unsortedBam, path_to_sortedBam)
         # fileno() method return the file descriptor number of tmp_stderr
         p = subprocess.Popen(