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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
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;
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