[med-svn] [trinityrnaseq] 01/03: more Jellyfish path fixes

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit ce5f9e7dd2ef1b9a6229046d6d8ee26fa56ed982
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Sun Feb 1 13:43:10 2015 -0500

    more Jellyfish path fixes
---
 debian/patches/jellyfish-path | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/debian/patches/jellyfish-path b/debian/patches/jellyfish-path
index 8f76187..3afec56 100644
--- a/debian/patches/jellyfish-path
+++ b/debian/patches/jellyfish-path
@@ -9,3 +9,25 @@
  my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
  my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
  my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/bin";
+--- trinityrnaseq.orig/util/insilico_read_normalization.pl
++++ trinityrnaseq/util/insilico_read_normalization.pl
+@@ -110,7 +110,7 @@
+ my $ROOTDIR = "$FindBin::RealBin/../";
+ my $UTILDIR = "$ROOTDIR/util/support_scripts/";
+ my $INCHWORM_DIR = "$ROOTDIR/Inchworm";
+-my $JELLYFISH_DIR = "$ROOTDIR/trinity-plugins/jellyfish";
++my $JELLYFISH_DIR = "/usr";
+ my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
+ 
+ unless (@ARGV) {
+--- trinityrnaseq.orig/util/misc/run_jellyfish.pl
++++ trinityrnaseq/util/misc/run_jellyfish.pl
+@@ -11,7 +11,7 @@
+ my $hash_size = $ARGV[1] or die $usage;
+ 
+ 
+-my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3";
++my $JELLYFISH_DIR = "/usr";
+ my $CPU = 4;
+ my $min_kmer_cov = 1;
+ 

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