[med-svn] [trinityrnaseq] 04/04: version bump; upstream dropped deps
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Sep 29 19:43:35 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch test/2.1.0
in repository trinityrnaseq.
commit d97ae6a7a44d239d5a739acb95da95cd189fe1c8
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Sep 29 12:16:01 2015 -0700
version bump; upstream dropped deps
patch refresh
---
debian/changelog | 2 +-
debian/control | 2 -
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 | 132 +++++++++------------
debian/patches/hardening | 4 +-
debian/patches/hashbang | 38 ------
debian/patches/jellyfish-path | 4 +-
debian/patches/noExitTester | 12 +-
debian/patches/update-paths | 26 +---
11 files changed, 75 insertions(+), 170 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f830a90..dc9f418 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-trinityrnaseq (2.0.6+dfsg-1) UNRELEASED; urgency=low
+trinityrnaseq (2.1.0+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #777697)
diff --git a/debian/control b/debian/control
index e071880..74936ce 100644
--- a/debian/control
+++ b/debian/control
@@ -34,10 +34,8 @@ Depends: ${shlibs:Depends},
jellyfish,
r-base-core,
r-bioc-edger,
- rsem,
berkeley-express,
trimmomatic,
- transdecoder,
parafly,
curl
Suggests: collectl
diff --git a/debian/patches/0001-fix_gcc5.patch.patch b/debian/patches/0001-fix_gcc5.patch.patch
index 1465d7e..1b91c9e 100644
--- a/debian/patches/0001-fix_gcc5.patch.patch
+++ b/debian/patches/0001-fix_gcc5.patch.patch
@@ -7,13 +7,11 @@ Add code for GCC 5 Compilation
Chrysalis/Makefile | 4 ++++
1 file changed, 4 insertions(+)
-diff --git a/Chrysalis/Makefile b/Chrysalis/Makefile
-index 448b2d1..11eae21 100644
---- a/Chrysalis/Makefile
-+++ b/Chrysalis/Makefile
-@@ -302,6 +302,10 @@ ifeq ($(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..cc63c9f 100644
--- a/debian/patches/fix_system_paths
+++ b/debian/patches/fix_system_paths
@@ -1,81 +1,55 @@
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
+@@ -22,7 +22,7 @@
+
+ BEGIN {
+
+- $ENV{TRINITY_HOME} = "$FindBin::Bin";
++ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
+
+ }
+
+@@ -444,7 +444,7 @@
+ # 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
+@@ -10,8 +10,8 @@
+ 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 +395,7 @@
+
+ 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);
+ }
+
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..def042b 100644
--- a/debian/patches/hashbang
+++ b/debian/patches/hashbang
@@ -41,41 +41,3 @@ 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
- ../../../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
- 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
- ../../../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
- 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
- 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..a41f67e 100644
--- a/debian/patches/noExitTester
+++ b/debian/patches/noExitTester
@@ -1,12 +1,12 @@
Description:NoExitTester
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -2193,32 +2193,6 @@
+@@ -2254,32 +2254,6 @@
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..8da06bb 100644
--- a/debian/patches/update-paths
+++ b/debian/patches/update-paths
@@ -5,31 +5,7 @@ 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
-
- #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 $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 $PARAFLY = "/usr/bin/ParaFly";
-+my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
- my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
-
-
-@@ -320,7 +320,7 @@
+@@ -324,7 +324,7 @@
### Butterfly-related options: ####
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
--
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