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Description:Jellyfish path
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
@@ -41,7 +41,7 @@
my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
-my $JELLYFISH_DIR = "$ROOTDIR/trinity-plugins/jellyfish";
+my $JELLYFISH_DIR = "/usr";
my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
--- 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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