[med-svn] [trinityrnaseq] 03/03: bump version, refresh patches
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Oct 22 16:41:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit ac69c098a85d207c6c82561ea8fa4f97d08b554b
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Thu Oct 22 08:32:12 2015 -0700
bump version, refresh patches
update builddeps & add overrides
license cleanup
---
debian/changelog | 4 +-
debian/control | 3 +-
debian/copyright | 14 +-
debian/patches/0001-fix_gcc5.patch.patch | 12 +-
debian/patches/0002-fix_istream_failure_call.patch | 11 +-
debian/patches/chrysalis-make-tweak | 2 +-
debian/patches/fix_system_paths | 168 +++++++++++----------
debian/patches/hardening | 4 +-
debian/patches/hashbang | 57 +++----
debian/patches/jellyfish-path | 4 +-
debian/patches/noExitTester | 12 +-
debian/patches/update-paths | 13 +-
debian/rules | 1 +
debian/trinityrnaseq-examples.lintian-overrides | 2 +
debian/trinityrnaseq.lintian-overrides | 2 +
15 files changed, 156 insertions(+), 153 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f830a90..6a64019 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-trinityrnaseq (2.0.6+dfsg-1) UNRELEASED; urgency=low
+trinityrnaseq (2.1.1+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #777697)
- -- Michael R. Crusoe <crusoe at ucdavis.edu> Wed, 16 Sep 2015 12:35:09 -0700
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Thu, 22 Oct 2015 08:31:56 -0700
diff --git a/debian/control b/debian/control
index e071880..f92f657 100644
--- a/debian/control
+++ b/debian/control
@@ -56,7 +56,8 @@ Package: trinityrnaseq-examples
Architecture: all
Depends: ${perl:Depends},
${java:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ r-base-core
Recommends: trinityrnaseq
Description: RNA-Seq De novo Assembly common example and testing files
Trinity represents a novel method for the efficient and robust de novo
diff --git a/debian/copyright b/debian/copyright
index a857477..afd60a0 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -19,8 +19,8 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
Files: *
Copyright: © 2011 The Broad Institute, Inc
© 2014 trinityrnaseq
-Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
License: BSD-3-clause
+Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
Files: Butterfly/src/src/NWalign.java
Copyright: Ahmed Moustafa <ahmed at users.sf.net>
@@ -28,12 +28,12 @@ License: GPL-2+
Files: trinity-plugins/fstrozzi-Fastool-7c3e034f05/kseq.h
Copyright: (c) 2008 Genome Research Ltd (GRL).
-License: MIT
+License: Expat
Files: trinity-plugins/*Fastool*
Copyright: (c) 2012 Francesco Strozzi
-Comment: https://github.com/fstrozzi/Fastool
License: Expat
+Comment: https://github.com/fstrozzi/Fastool
Files: debian/*
Copyright: (c) 2015 Michigan State University
@@ -75,10 +75,10 @@ License: Expat
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
- .
+ .
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
- .
+ .
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
@@ -118,10 +118,10 @@ License: MIT
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
- .
+ .
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
- .
+ .
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
diff --git a/debian/patches/0001-fix_gcc5.patch.patch b/debian/patches/0001-fix_gcc5.patch.patch
index 1465d7e..1b91c9e 100644
--- a/debian/patches/0001-fix_gcc5.patch.patch
+++ b/debian/patches/0001-fix_gcc5.patch.patch
@@ -7,13 +7,11 @@ Add code for GCC 5 Compilation
Chrysalis/Makefile | 4 ++++
1 file changed, 4 insertions(+)
-diff --git a/Chrysalis/Makefile b/Chrysalis/Makefile
-index 448b2d1..11eae21 100644
---- a/Chrysalis/Makefile
-+++ b/Chrysalis/Makefile
-@@ -302,6 +302,10 @@ ifeq ($(COMPILER),g++)
- ifeq ($(GPP_MAJOR_VERSION),4)
- SYS_INCS = -iquote . $(XERCES_INC)
+--- trinityrnaseq.orig/Chrysalis/Makefile
++++ trinityrnaseq/Chrysalis/Makefile
+@@ -305,6 +305,10 @@
+ ifeq ($(GPP_MAJOR_VERSION),5)
+ SYS_INCS = -iquote . $(XERCES_INC)
endif
+ ifeq ($(GPP_MAJOR_VERSION),5)
+ SYS_INCS = -iquote . $(XERCES_INC)
diff --git a/debian/patches/0002-fix_istream_failure_call.patch b/debian/patches/0002-fix_istream_failure_call.patch
index a6ccaf9..d8ed6a9 100644
--- a/debian/patches/0002-fix_istream_failure_call.patch
+++ b/debian/patches/0002-fix_istream_failure_call.patch
@@ -8,16 +8,13 @@ of calling fail() method
Inchworm/src/sequenceUtil.cpp | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
-diff --git a/Inchworm/src/sequenceUtil.cpp b/Inchworm/src/sequenceUtil.cpp
-index 7ba9c1f..a24c250 100644
---- a/Inchworm/src/sequenceUtil.cpp
-+++ b/Inchworm/src/sequenceUtil.cpp
-@@ -52,7 +52,8 @@ bool contains_non_gatc (string kmer) {
+--- trinityrnaseq.orig/Inchworm/src/sequenceUtil.cpp
++++ trinityrnaseq/Inchworm/src/sequenceUtil.cpp
+@@ -52,7 +52,7 @@
string read_sequence_from_file (string filename) {
ifstream fileReader (filename.c_str());
-- if (fileReader == 0) { // couldn't open file
-+ //if (fileReader == 0) { // couldn't open file
+- if (!fileReader) { // couldn't open file
+ if (fileReader.fail()) { // couldn't open file
throw(stacktrace() + "\n\nCould not open " + filename + "\n");
}
diff --git a/debian/patches/chrysalis-make-tweak b/debian/patches/chrysalis-make-tweak
index 093c9ca..44a13c7 100644
--- a/debian/patches/chrysalis-make-tweak
+++ b/debian/patches/chrysalis-make-tweak
@@ -7,7 +7,7 @@ Last-Update: 2015-02-16
--- trinityrnaseq.orig/Chrysalis/Makefile
+++ trinityrnaseq/Chrysalis/Makefile
-@@ -432,7 +432,7 @@
+@@ -435,7 +435,7 @@
for file in $(EXECUTABLES); do rm -f $(BIN)/$$file; done
rm -f MakeDepend $(BIN)/MakeDepend contigs.out my.permanent.log.file \
core a.out Makefile.bak bsubin BasevectorTables.h $(BIN)/checkLock
diff --git a/debian/patches/fix_system_paths b/debian/patches/fix_system_paths
index 0464241..fb7780e 100644
--- a/debian/patches/fix_system_paths
+++ b/debian/patches/fix_system_paths
@@ -1,81 +1,91 @@
Description: drop some use of FindBin and hardcode paths
Author: Tim Booth <tbooth at ceh.ac.uk>
---- a/util/align_and_estimate_abundance.pl
-+++ b/util/align_and_estimate_abundance.pl
-@@ -2,15 +2,14 @@
-
- use strict;
- use warnings;
--use FindBin;
-
- use Cwd;
-
- use Getopt::Long qw(:config no_ignore_case bundling pass_through);
-
-
--my $RSEM_DIR = "$FindBin::Bin/../trinity-plugins/rsem";
--$ENV{PATH} = "$RSEM_DIR:$ENV{PATH}"; # be sure to use the included rsem package over other ones installed.
-+my $DM_DIR = "/usr/lib/debian-med/bin";
-+$ENV{PATH} = "$DM_DIR:$ENV{PATH}"; # be sure to find the right express executable
-
-
- my %aligner_params = ( 'bowtie_RSEM' => '--all --best --strata -m 300 --chunkmbs 512',
-@@ -352,7 +351,7 @@
-
- if ($trinity_mode && ! $gene_trans_map_file) {
- $gene_trans_map_file = "$transcripts.gene_trans_map";
-- my $cmd = "$FindBin::Bin/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file";
-+ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl '$transcripts' > '$gene_trans_map_file'";
- &process_cmd($cmd) unless (-e $gene_trans_map_file);
- }
-
-@@ -576,7 +575,7 @@
- sub make_eXpress_genes_file {
- my ($results_xprs_file, $gene_to_trans_map_file) = @_;
-
-- my $cmd = "$FindBin::Bin/support_scripts/eXpress_trans_to_gene_results.pl $results_xprs_file $gene_to_trans_map_file > $results_xprs_file.genes";
-+ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/eXpress_trans_to_gene_results.pl '$results_xprs_file' '$gene_to_trans_map_file' > '$results_xprs_file.genes'";
- &process_cmd($cmd);
-
- return;
---- a/Trinity
-+++ b/Trinity
-@@ -5,8 +5,7 @@
- use threads;
- no strict qw(subs refs);
-
--use FindBin;
--use lib ("$FindBin::Bin/PerlLib");
-+use lib ("/usr/lib/trinityrnaseq/PerlLib");
- use File::Basename;
- use Time::localtime;
- use Cwd;
-@@ -22,7 +21,7 @@
-
- BEGIN {
-
-- $ENV{TRINITY_HOME} = "$FindBin::Bin";
-+ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
-
- }
-
-@@ -440,7 +439,7 @@
- # Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
- # --genome_guided_max_intron 10000 --CPU 6
- #
--# see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
-+# see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
- # for sample data and 'runMe.sh' for example Trinity execution
- #
- # For more details, visit: http://trinityrnaseq.github.io
---- a/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
-+++ b/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
-@@ -8,7 +8,7 @@
- use FindBin;
- use File::Basename;
-
--$ENV{PATH} .= ":$FindBin::Bin/../../trinity-plugins/slclust/bin/";
-+$ENV{PATH} .= ":/usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/";
-
- my $help_flag;
-
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
+@@ -8,7 +8,7 @@
+ use FindBin;
+ use File::Basename;
+
+-$ENV{PATH} .= ":$FindBin::Bin/../../trinity-plugins/slclust/bin/";
++$ENV{PATH} .= ":/usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/";
+
+ my $help_flag;
+
+--- trinityrnaseq.orig/Trinity
++++ trinityrnaseq/Trinity
+@@ -5,8 +5,7 @@
+ use threads;
+ no strict qw(subs refs);
+
+-use FindBin;
+-use lib ("$FindBin::RealBin/PerlLib");
++use lib ("/usr/lib/trinityrnaseq/PerlLib");
+ use File::Basename;
+ use Time::localtime;
+ use Cwd;
+@@ -22,7 +21,7 @@
+
+ BEGIN {
+
+- $ENV{TRINITY_HOME} = "$FindBin::Bin";
++ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
+
+ }
+
+@@ -444,7 +443,7 @@
+ # Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
+ # --genome_guided_max_intron 10000 --CPU 6
+ #
+-# see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
++# see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
+ # for sample data and 'runMe.sh' for example Trinity execution
+ #
+ # For more details, visit: http://trinityrnaseq.github.io
+--- trinityrnaseq.orig/util/align_and_estimate_abundance.pl
++++ trinityrnaseq/util/align_and_estimate_abundance.pl
+@@ -2,7 +2,6 @@
+
+ use strict;
+ use warnings;
+-use FindBin;
+
+ use Cwd;
+ use Carp;
+@@ -10,8 +9,8 @@
+ use Getopt::Long qw(:config no_ignore_case bundling pass_through);
+
+
+-my $RSEM_DIR = "$FindBin::Bin/../trinity-plugins/rsem";
+-$ENV{PATH} = "$RSEM_DIR:$ENV{PATH}"; # be sure to use the included rsem package over other ones installed.
++my $DM_DIR = "/usr/lib/debian-med/bin";
++$ENV{PATH} = "$DM_DIR:$ENV{PATH}"; # be sure to find the right express executable
+
+
+ my %aligner_params = (
+@@ -395,7 +394,7 @@
+
+ if ($trinity_mode && ! $gene_trans_map_file) {
+ $gene_trans_map_file = "$transcripts.gene_trans_map";
+- my $cmd = "$FindBin::Bin/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file";
++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl '$transcripts' > '$gene_trans_map_file'";
+ &process_cmd($cmd) unless (-e $gene_trans_map_file);
+ }
+
+@@ -636,7 +635,7 @@
+
+ if ($gene_trans_map_file) {
+
+- my $cmd = "$FindBin::Bin/support_scripts/eXpress_trans_to_gene_results.pl results.xprs $gene_trans_map_file > results.xprs.genes";
++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/eXpress_trans_to_gene_results.pl results.xprs $gene_trans_map_file > results.xprs.genes";
+ &process_cmd($cmd);
+ }
+
+@@ -792,7 +791,7 @@
+
+ if ($gene_trans_map_file) {
+
+- my $cmd = "$FindBin::Bin/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes";
++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes";
+ &process_cmd($cmd);
+ }
+
diff --git a/debian/patches/hardening b/debian/patches/hardening
index 22ac52d..eefba7b 100644
--- a/debian/patches/hardening
+++ b/debian/patches/hardening
@@ -2,7 +2,7 @@ Description: Use LDFLAGS & CPPFLAGS to enable hardening
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
--- trinityrnaseq.orig/Chrysalis/Makefile
+++ trinityrnaseq/Chrysalis/Makefile
-@@ -309,7 +309,7 @@
+@@ -312,7 +312,7 @@
endif
# Linking control (e.g. to link templates):
@@ -11,7 +11,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
# Required libraries:
SYS_LIBS = -lm -pthread
-@@ -381,7 +381,8 @@
+@@ -384,7 +384,8 @@
$(SYS_LANG) \
$(SYS_INCS) \
$(OMP_OPTIONS) \
diff --git a/debian/patches/hashbang b/debian/patches/hashbang
index 4f606f2..1a0eb2b 100644
--- a/debian/patches/hashbang
+++ b/debian/patches/hashbang
@@ -41,41 +41,34 @@ Description: add #! lines as needed
+#!/bin/sh
../../Trinity.pl --seqType fq --left ex9.reads.left.fq --right ex9.reads.right.fq --SS_lib_type RF --bfly_opts "--edge-thr=0.05 --stderr -V 18" --run_butterfly --output trinity_outdir
---- trinityrnaseq.orig/sample_data/test_align_and_estimate_abundance/run_eXpress.sh
-+++ trinityrnaseq/sample_data/test_align_and_estimate_abundance/run_eXpress.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
- ../../util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --gene_trans_map Trinity.fasta.gene_trans_map --aln_method bowtie --est_method eXpress --output_dir eXpress_estimate --SS_lib_type RF
---- trinityrnaseq.orig/sample_data/test_align_and_estimate_abundance/run_rsem.sh
-+++ trinityrnaseq/sample_data/test_align_and_estimate_abundance/run_rsem.sh
-@@ -1,3 +1,4 @@
-+#!/bin/sh
- if [ ! -e Trinity.fasta ]; then
- gunzip -c Trinity.fasta.gz > Trinity.fasta
- fi
---- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/run_DESeq2.sh
-+++ trinityrnaseq/sample_data/test_edgeR_diff_expr/example_DESeq2_analysis_pipeline/run_DESeq2.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
+--- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
++++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
+@@ -1 +1,3 @@
++#! /bin/sh
++
../../../Analysis/DifferentialExpression/run_DE_analysis.pl --matrix counts.matrix --samples_file samples.txt --method DESeq2
---- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/cleanMe.sh
-+++ trinityrnaseq/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/cleanMe.sh
-@@ -1,2 +1,3 @@
-+#!/bin/sh
+--- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
++++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
+@@ -1,2 +1,4 @@
++#! /bin/sh
++
rm -rf ./edgeR.*.dir
---- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/runMe.sh
-+++ trinityrnaseq/sample_data/test_edgeR_diff_expr/example_edgeR_analysis_pipeline/runMe.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
+--- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
++++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
+@@ -1 +1,3 @@
++#! /bin/sh
++
../../../Analysis/DifferentialExpression/run_DE_analysis.pl --matrix example.matrix --method edgeR
---- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/cleanMe.sh
-+++ trinityrnaseq/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/cleanMe.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
+--- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/cleanMe.sh
++++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/cleanMe.sh
+@@ -1 +1,3 @@
++#! /bin/sh
++
rm -f MA_plot.eps diff_expr.results.txt
---- trinityrnaseq.orig/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/runMe.sh
-+++ trinityrnaseq/sample_data/test_edgeR_diff_expr/testEdgeRfuncs/runMe.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
+--- trinityrnaseq.orig/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
++++ trinityrnaseq/sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
+@@ -1 +1,3 @@
++#! /bin/sh
++
R --vanilla -q < run_edgeR_on_sample_data.R
diff --git a/debian/patches/jellyfish-path b/debian/patches/jellyfish-path
index aca6a33..8887730 100644
--- a/debian/patches/jellyfish-path
+++ b/debian/patches/jellyfish-path
@@ -1,7 +1,7 @@
Description:Jellyfish path
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -38,7 +38,7 @@
+@@ -41,7 +41,7 @@
my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
@@ -9,7 +9,7 @@ Description:Jellyfish path
+my $JELLYFISH_DIR = "/usr";
my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
- my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/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 @@
diff --git a/debian/patches/noExitTester b/debian/patches/noExitTester
index 628311a..c2f0759 100644
--- a/debian/patches/noExitTester
+++ b/debian/patches/noExitTester
@@ -1,12 +1,12 @@
Description:NoExitTester
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -2193,32 +2193,6 @@
+@@ -2260,32 +2260,6 @@
die "Error, cannot find 'java'. Please be sure it is available within your \${PATH} setting and then try again.";
}
-
-- my $cmd = "java -Xmx64m -jar $UTILDIR/support_scripts/ExitTester.jar 0";
+- my $cmd = "java -Xmx64m -XX:ParallelGCThreads=$bflyGCThreads -jar $UTILDIR/support_scripts/ExitTester.jar 0";
- eval {
- &process_cmd($cmd);
- };
@@ -18,19 +18,19 @@ Description:NoExitTester
-
- }
-
-- $cmd = "java -Xmx64m -jar $UTILDIR/support_scripts/ExitTester.jar 1";
+- $cmd = "java -Xmx64m -XX:ParallelGCThreads=$bflyGCThreads -jar $UTILDIR/support_scripts/ExitTester.jar 1";
- eval {
- &process_cmd($cmd);
- };
-
- if ($@) {
-- print "-we properly captured the java failure status, as needed. Looking good.\n" if $SEE;
+- print "-we properly captured the java failure status, as needed. Looking good.\n" if $VERBOSE;
- }
- else {
- print STDERR "-we are unable to properly capture java failure status. Please be sure that java (or any wrapper around java that's being used) can properly capture and propagate failure status before proceeding.\n";
- exit(1);
- }
-
- print "Java tests succeeded.\n" if $SEE;
- print "###################################\n\n" if $SEE;
+ print "Java tests succeeded.\n" if $VERBOSE;
+ print "###################################\n\n" if $VERBOSE;
diff --git a/debian/patches/update-paths b/debian/patches/update-paths
index 7546420..1711bfd 100644
--- a/debian/patches/update-paths
+++ b/debian/patches/update-paths
@@ -5,8 +5,8 @@ Last-Updated: 2015-02-22
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -32,18 +32,18 @@
- open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
+@@ -35,17 +35,17 @@
+
#directory defnintions
-my $ROOTDIR = "$FindBin::RealBin";
@@ -16,20 +16,19 @@ Last-Updated: 2015-02-22
my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
-my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
-+my $BUTTERFLY_DIR = "/usr/share/java";
++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 $COLLECTL_DIR = "/usr/bin";
- my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/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";
-
-@@ -320,7 +320,7 @@
+ $ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
+@@ -324,7 +324,7 @@
### Butterfly-related options: ####
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
diff --git a/debian/rules b/debian/rules
index abcde6e..af0b1d0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -54,6 +54,7 @@ override_dh_install:
${EXBASEDIR}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh
chmod -R a-x ${BASEDIR}/PerlLib/*.pm
chmod -R a-x ${BASEDIR}/PerlLib/*/*.pm
+ chmod a-x ${BASEDIR}/util/support_scripts/tests/test.py
get-orig-source:
uscan --verbose --force-download --repack --compression xz
diff --git a/debian/trinityrnaseq-examples.lintian-overrides b/debian/trinityrnaseq-examples.lintian-overrides
new file mode 100644
index 0000000..7154e41
--- /dev/null
+++ b/debian/trinityrnaseq-examples.lintian-overrides
@@ -0,0 +1,2 @@
+# Shipped from upstream, timestamp not a problem
+trinityrnaseq-examples: package-contains-timestamped-gzip usr/share/trinityrnaseq/sample_data/*.gz
diff --git a/debian/trinityrnaseq.lintian-overrides b/debian/trinityrnaseq.lintian-overrides
new file mode 100644
index 0000000..bec3f2b
--- /dev/null
+++ b/debian/trinityrnaseq.lintian-overrides
@@ -0,0 +1,2 @@
+# shipped by upstream, no problem to be timestamped
+trinityrnaseq: package-contains-timestamped-gzip usr/lib/trinityrnaseq/Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
--
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