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Description: Updates the main Trinity program to use FHS paths
Author: Michael R. Crusoe <mcrusoe@msu.edu>
Forwarded: no
Last-Updated: 2015-02-22
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
@@ -35,17 +35,17 @@
#directory defnintions
-my $ROOTDIR = "$FindBin::RealBin";
+my $ROOTDIR = "/usr/lib/trinityrnaseq";
my $UTILDIR = "$ROOTDIR/util";
my $MISCDIR = "$UTILDIR/misc";
my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
-my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
+my $BUTTERFLY_DIR = "/usr/share/java/";
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";
-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
+my $COLLECTL_DIR = "/usr/bin";
+my $PARAFLY = "/usr/bin/ParaFly";
+my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
$ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
@@ -325,7 +325,7 @@
### Butterfly-related options: ####
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
-# (see butterfly options: java -jar Butterfly.jar ).
+# (see butterfly options: java -jar /usr/share/java/Butterfly.jar ).
# (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).
#
# //////////////////////////////////
--- trinityrnaseq.orig/Chrysalis/analysis/Chrysalis.cc
+++ trinityrnaseq/Chrysalis/analysis/Chrysalis.cc
@@ -258,7 +258,7 @@
commandArg<string> iwormStringCmmd("-iworm","inchworm file", "");
commandArg<string> oStringCmmd("-o","output directory");
commandArg<bool> pairsStringCmmd("-paired", "paired-end reads are used.", false);
- commandArg<string> butterflyCmmd("-butterfly","butterfly executable", "../Butterfly/Butterfly.jar");
+ commandArg<string> butterflyCmmd("-butterfly","butterfly executable", "/usr/share/java/Butterfly.jar");
commandArg<bool> skipCmmd("-skip","skip initial 2 steps", false);
commandArg<bool> strandCmmd("-strand","strand-specific data", false);
commandArg<bool> nobreakCmmd("-nobreak","skip breaking", false);
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