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
@@ -35,24 +35,21 @@
 
 
 #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 $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/COLLECTL/collectl";
+my $BUTTERFLY_DIR = "/usr/share/java";
+my $COLLECTL_DIR = "/usr/bin";
 my $TRINITY_BIN_DIR = "$ROOTDIR/trinity-plugins/BIN";
-my $PARAFLY = "$TRINITY_BIN_DIR/ParaFly";
-my $HTSLIB_DIR = "$ROOTDIR/trinity-plugins/htslib";
-
-$ENV{LD_LIBRARY_PATH} .= ":${HTSLIB_DIR}";
+my $PARAFLY = "/usr/bin/ParaFly";
 
 if ($ENV{TRINITY_NO_RETRIES}) {
     $PARAFLY .= " -max_retry 1 ";
 }
 
-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
+my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
 my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
 
 $ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
@@ -367,7 +364,7 @@
 #  --bfly_algorithm <string>       : assembly algorithm to use. Options: @BFLY_ALGORITHMS
 #
 #  --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);
--- trinityrnaseq.orig/trinity-plugins/bamsifter/Makefile
+++ trinityrnaseq/trinity-plugins/bamsifter/Makefile
@@ -1,2 +1,3 @@
+CXX ?= g++
 sift_bam_max_cov: sift_bam_max_cov.cpp
-	g++ sift_bam_max_cov.cpp -Wall -lhts -O2 -I../htslib -L../htslib -o bamsifter
+	$(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) sift_bam_max_cov.cpp -Wall -lhts -O2 -o bamsifter
