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Description: Updates the main Trinity program to use FHS paths
Author: Michael R. Crusoe <crusoe@debian.org>
Forwarded: not-needed
Last-Updated: 2015-02-22
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
@@ -381,7 +381,7 @@
# --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).
#
#
@@ -1074,7 +1074,7 @@
}
unless ($BFLY_JAR) {
- $BFLY_JAR = "$BUTTERFLY_DIR/Butterfly.jar";
+ $BFLY_JAR = "/usr/share/java/Butterfly.jar";
}
--- 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
@@ -3,7 +3,7 @@
cwd = $(shell pwd)
sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h
- g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts
+ $(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts
htslib/version.h :
--- trinityrnaseq.orig/util/misc/bam_gene_tests/write_trin_cmds.pl
+++ trinityrnaseq/util/misc/bam_gene_tests/write_trin_cmds.pl
@@ -23,7 +23,7 @@
# Example:
#
-# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar ~/SVN/trinityrnaseq/trunk/Butterfly/Butterfly.jar --JM 1G --seqType fa
+# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar /usr/share/java/Butterfly.jar --JM 1G --seqType fa
__EOUSAGE__
--- trinityrnaseq.orig/util/misc/compare_bflies.pl
+++ trinityrnaseq/util/misc/compare_bflies.pl
@@ -37,7 +37,7 @@
my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
&process_cmd($cmd);
- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/prev_vers/Butterfly_r2013_08_14.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
+ $cmd = "java -Xmx4G -jar $/usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
open (my $ofh, ">bfly.cmd") or die $!;
print $ofh $cmd;
@@ -61,7 +61,7 @@
&process_cmd($cmd);
- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
+ $cmd = "java -Xmx4G -jar /usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
open (my $ofh, ">bfly.cmd") or die $!;
print $ofh $cmd;
--- trinityrnaseq.orig/util/misc/sim_test_framework/run_Trinity_eval.pl
+++ trinityrnaseq/util/misc/sim_test_framework/run_Trinity_eval.pl
@@ -17,7 +17,7 @@
my $help_flag;
my $ref_trans_fa;
-my $BFLY_JAR = "$ENV{TRINITY_HOME}/Butterfly/Butterfly.jar";
+my $BFLY_JAR = "/usr/share/java/Butterfly.jar";
my $INCLUDE_REF_TRANS = 0;
my $OUT_DIR = "testing_dir";
my $MIN_CONTIG_LENGTH = 200;
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