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
@@ -31,16 +31,16 @@
 
 
 #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 $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/COLLECTL/collectl";
-my $PARAFLY = "$ROOTDIR/trinity-plugins/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}";
@@ -330,7 +330,7 @@
 ###  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);
