# HG changeset patch
# User mvdbeek
# Date 1434028055 14400
# Node ID d123b6e6a633acbaccb7568cf155440d344d801f
# Parent  0975f22678097442f7ab3f88014beef138e5b90d
planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r 0975f2267809 -r d123b6e6a633 sRbowtie.py
--- 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(