[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-30-gf1b8a64

[Carlos Borroto]

The following commit has been merged in the master branch:
commit d6b7dd794a5613ebf77a5a531c71dc90bf7f32a7
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Thu Jun 21 14:30:15 2012 -0400

    patch bashism_in_shell_script refreshed

diff --git a/debian/patches/bashism_in_shell_script.patch b/debian/patches/bashism_in_shell_script.patch
index 2e79ad6..9df6b3c 100644
--- a/debian/patches/bashism_in_shell_script.patch
+++ b/debian/patches/bashism_in_shell_script.patch
@@ -2,10 +2,12 @@ Author: Andreas Tille <tille at debian.org>
 Bug-Closed: http://bugs.debian.org/671813
 Descriptions: Remove bashism from shell script
 
---- tophat.orig/src/tophat2.in
-+++ tophat/src/tophat2.in
+Index: tophat/src/tophat2.in
+===================================================================
+--- tophat.orig/src/tophat2.in	2012-06-21 14:28:32.730584269 -0400
++++ tophat/src/tophat2.in	2012-06-21 14:28:47.166584998 -0400
 @@ -1,9 +1,9 @@
- #!/bin/sh
+ #!/bin/bash
  prefix="__PREFIX__"
  pbin=""
 -if [[ -z $prefix ]]; then

-- 
A spliced read mapper for RNA-Seq