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Author: Michael R. Crusoe
Description: Match the Debian's path
--- a/Trinity
+++ b/Trinity
@@ -52,8 +52,8 @@ if ($ENV{TRINITY_NO_RETRIES}) {
$PARAFLY .= " -max_retry 1 ";
}
-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
-my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
+my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
+my $TRIMMOMATIC_DIR = "/usr/share/trimmomatic";
$ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
@@ -198,7 +198,7 @@ my $NO_PARALLEL_IWORM = 0;
## 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; ## now on by default, unless told not to via --no_normalize_reads! See below for logic.
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