[med-svn] [trinityrnaseq] 02/03: adjust path to trimmomatic adapters

[Michael Crusoe]

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

commit 77de52d9e7b24fadb5d5de86eb2565fc573e0134
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 15 06:31:57 2016 -0800

    adjust path to trimmomatic adapters
---
 debian/patches/adjust-trimmomatic-adapters-path | 13 +++++++++++++
 debian/patches/series                           |  1 +
 2 files changed, 14 insertions(+)

diff --git a/debian/patches/adjust-trimmomatic-adapters-path b/debian/patches/adjust-trimmomatic-adapters-path
new file mode 100644
index 0000000..bdd4a53
--- /dev/null
+++ b/debian/patches/adjust-trimmomatic-adapters-path
@@ -0,0 +1,13 @@
+Author: Michael R. Crusoe
+Description: Match the Debian's path
+--- trinityrnaseq.orig/Trinity
++++ trinityrnaseq/Trinity
+@@ -193,7 +193,7 @@
+ 
+ ## Quality trimming params
+ my $RUN_TRIMMOMATIC_FLAG = 0;
+-my $trimmomatic_quality_trim_params = "ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25";
++my $trimmomatic_quality_trim_params = "ILLUMINACLIP:$TRIMMOMATIC_DIR/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25";
+ 
+ ## Normalize reads
+ my $NORMALIZE_READS_FLAG = 0;
diff --git a/debian/patches/series b/debian/patches/series
index dcd2222..bb78d37 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -13,3 +13,4 @@ hardening
 reproducible-build
 scaffold_iworm_contigs-Makefile-fix-clean
 disable-version-check
+adjust-trimmomatic-adapters-path

-- 
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