[med-svn] [trinityrnaseq] 01/01: add bowtie dependency & update trimmomatic path

[Michael Crusoe]

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

commit a1941bc6953eda5af0a2128bcdd73bf0c5b57245
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 15 14:24:51 2016 -0800

    add bowtie dependency & update trimmomatic path
---
 debian/control                                  | 1 +
 debian/patches/adjust-trimmomatic-adapters-path | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/debian/control b/debian/control
index 5d5f354..4d2ab61 100644
--- a/debian/control
+++ b/debian/control
@@ -27,6 +27,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${perl:Depends},
          ${java:Depends},
+         bowtie,
          bowtie2,
          python,
          libwww-perl,
diff --git a/debian/patches/adjust-trimmomatic-adapters-path b/debian/patches/adjust-trimmomatic-adapters-path
index bdd4a53..e787ec8 100644
--- a/debian/patches/adjust-trimmomatic-adapters-path
+++ b/debian/patches/adjust-trimmomatic-adapters-path
@@ -2,6 +2,15 @@ Author: Michael R. Crusoe
 Description: Match the Debian's path
 --- trinityrnaseq.orig/Trinity
 +++ trinityrnaseq/Trinity
+@@ -45,7 +45,7 @@
+ my $COLLECTL_DIR = "/usr/bin";
+ my $PARAFLY = "/usr/bin/ParaFly";
+ my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
+-my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
++my $TRIMMOMATIC_DIR = "/usr/share/Trimmomatic";
+ 
+ $ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
+ 
 @@ -193,7 +193,7 @@
  
  ## Quality trimming params

-- 
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