[med-svn] [trinityrnaseq] 03/03: new upstream release
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri May 20 13:32:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit 11fefd4359dd64a75f094b7ce8d31fa92d7cdb6b
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Fri May 20 01:47:12 2016 -0700
new upstream release
---
debian/changelog | 11 ++-
debian/control | 2 +-
debian/patches/chrysalis-make-tweak | 18 ----
debian/patches/disable-version-check | 2 +-
debian/patches/fix_system_paths | 42 +++++-----
debian/patches/hardening | 98 ----------------------
debian/patches/hashbang | 43 ----------
debian/patches/noExitTester | 2 +-
debian/patches/reproducible-build | 22 -----
.../scaffold_iworm_contigs-Makefile-fix-clean | 17 ----
debian/patches/series | 6 --
debian/patches/skip-kallisto-deseq2-tests | 30 +------
debian/patches/spelling | 35 --------
debian/patches/update-paths | 2 +-
debian/rules | 3 +-
debian/trinityrnaseq.docs | 1 -
16 files changed, 35 insertions(+), 299 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 0e13851..1c7b85d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,16 @@
-trinityrnaseq (2.1.1+dfsg2-2) UNRELEASED; urgency=medium
+trinityrnaseq (2.2.0+dfsg-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Team upload
* d/watch: Use xz compression for upstream source
- -- Andreas Tille <tille at debian.org> Fri, 20 May 2016 09:41:52 +0200
+ [ Michael R. Crusoe ]
+ * new upstream version
+ * prune d/copyright excludes
+ * refresh patches, drop a few included upstream
+ * Standards-Version: '3.9.7' -> '3.9.8'
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 20 May 2016 01:46:16 -0700
trinityrnaseq (2.1.1+dfsg2-1) unstable; urgency=low
diff --git a/debian/control b/debian/control
index b64b6ba..fb6bd45 100644
--- a/debian/control
+++ b/debian/control
@@ -16,7 +16,7 @@ Build-Depends: debhelper (>= 9),
libjs-jquery,
jaligner,
libhts-dev
-Standards-Version: 3.9.7
+Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trinityrnaseq.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/trinityrnaseq.git
Homepage: http://trinityrnaseq.github.io/
diff --git a/debian/patches/chrysalis-make-tweak b/debian/patches/chrysalis-make-tweak
deleted file mode 100644
index 44a13c7..0000000
--- a/debian/patches/chrysalis-make-tweak
+++ /dev/null
@@ -1,18 +0,0 @@
-Description: don't die if a file is missing
-Author: Michael R. Crusoe <mcrusoe at msu.edu>
-
----
-
-Last-Update: 2015-02-16
-
---- trinityrnaseq.orig/Chrysalis/Makefile
-+++ trinityrnaseq/Chrysalis/Makefile
-@@ -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
-- find $(OBJ) -name '*.o' -exec rm {} \;
-+ find $(OBJ) -name '*.o' -exec rm {} \; || /bin/true
- rm -rf cxx_repository
- rm -f lib_*_temp.a
-
diff --git a/debian/patches/disable-version-check b/debian/patches/disable-version-check
index a3b388a..56a3c15 100644
--- a/debian/patches/disable-version-check
+++ b/debian/patches/disable-version-check
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Disable the version "phone home" for privacy
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -552,7 +552,7 @@
+@@ -553,7 +553,7 @@
my $ANANAS_DIR = "";
diff --git a/debian/patches/fix_system_paths b/debian/patches/fix_system_paths
index fb7780e..e5a7712 100644
--- a/debian/patches/fix_system_paths
+++ b/debian/patches/fix_system_paths
@@ -6,7 +6,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use FindBin;
use File::Basename;
--$ENV{PATH} .= ":$FindBin::Bin/../../trinity-plugins/slclust/bin/";
+-$ENV{PATH} .= ":$FindBin::RealBin/../../trinity-plugins/slclust/bin/";
+$ENV{PATH} .= ":/usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/";
my $help_flag;
@@ -27,12 +27,12 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
BEGIN {
-- $ENV{TRINITY_HOME} = "$FindBin::Bin";
+- $ENV{TRINITY_HOME} = "$FindBin::RealBin";
+ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
}
-@@ -444,7 +443,7 @@
+@@ -445,7 +444,7 @@
# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
# --genome_guided_max_intron 10000 --CPU 6
#
@@ -51,41 +51,39 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
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 @@
+@@ -399,7 +398,7 @@
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'";
+- my $cmd = "$FindBin::RealBin/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 $gene_trans_map_file);
}
-@@ -636,7 +635,7 @@
+@@ -663,7 +662,7 @@
if ($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 $cmd = "$FindBin::RealBin/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 @@
+@@ -821,7 +820,7 @@
- if ($gene_trans_map_file) {
+ if ( ($left || $single) && $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 $cmd = "$FindBin::RealBin/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);
}
+@@ -898,7 +897,7 @@
+
+ if ( ($left || $single) && $gene_trans_map_file) {
+
+- my $cmd = "$FindBin::RealBin/support_scripts/salmon_trans_to_gene_results.pl $output_dir/quant.sf $gene_trans_map_file > $output_dir/quant.sf.genes";
++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/salmon_trans_to_gene_results.pl $output_dir/quant.sf $gene_trans_map_file > $output_dir/quant.sf.genes";
+ &process_cmd($cmd);
+ }
+
diff --git a/debian/patches/hardening b/debian/patches/hardening
deleted file mode 100644
index 3803561..0000000
--- a/debian/patches/hardening
+++ /dev/null
@@ -1,98 +0,0 @@
-Description: Use LDFLAGS & CPPFLAGS to enable hardening
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- trinityrnaseq.orig/Chrysalis/Makefile
-+++ trinityrnaseq/Chrysalis/Makefile
-@@ -308,7 +308,7 @@
- endif
-
- # Linking control (e.g. to link templates):
--SYS_LINK =
-+SYS_LINK = $(LDFLAGS)
-
- # Required libraries:
- SYS_LIBS = -lm -pthread
-@@ -380,7 +380,8 @@
- $(SYS_LANG) \
- $(SYS_INCS) \
- $(OMP_OPTIONS) \
-- $(PTHREAD_OPTIONS)
-+ $(PTHREAD_OPTIONS) \
-+ $(CPPFLAGS)
-
- LINK_OPTIONS = \
- $(SYS_DEBUG) \
-@@ -466,7 +467,7 @@
- # How to compile C++ files:
- .cc.o:
- @ mkdir -p $(OBJ)/${@D}
-- $(CPLUSPLUS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o
-+ $(CPLUSPLUS) $(CXXFLAGS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o
-
- ##############################################################################
- ## ADDITIONAL TARGETS:
---- trinityrnaseq.orig/trinity-plugins/fstrozzi-Fastool-7c3e034f05/Makefile
-+++ trinityrnaseq/trinity-plugins/fstrozzi-Fastool-7c3e034f05/Makefile
-@@ -1,8 +1,7 @@
--CC = gcc
--CFLAGS = -O2 -std=c99 -Werror
-+CFLAGS += -O2 -std=c99 -Werror
-
- all:kseq.h fastool.c
-- $(CC) $(CFLAGS) fastool.c -o fastool
-+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) fastool.c -o fastool
-
- clean:
- rm -f *.o fastool
---- trinityrnaseq.orig/trinity-plugins/slclust/src/Makefile
-+++ trinityrnaseq/trinity-plugins/slclust/src/Makefile
-@@ -17,11 +17,8 @@
- # use ${LIBDIR} defined above if appropriate
- LIBS =
-
--# How they are invoked on the compile line (eg: -lspecial)
--LLIBS =
--
- # Local additions for the CFLAG options
--LOCAL_CFLAGS = -Wall
-+LOCAL_CXXFLAGS = -Wall
- #-static
-
-
-@@ -34,20 +31,11 @@
- INCLUDE = ${PROJECT_ROOT}/include
-
- DEBUG = DEBUG
--CFLAGS = -I${INCLUDE} ${LOCAL_CFLAGS}
--CC = g++ ${CFLAGS}
-+CXXFLAGS += -I${INCLUDE} ${LOCAL_CXXFLAGS}
-
- MAKEFILE = Makefile
-
-
--# Suffix rules
--
--.cc.o:
-- ${CC} -c $<
--
--.cpp.o:
-- ${CC} -c $<
--
- # Target dependencies
-
-
-@@ -59,12 +47,13 @@
-
-
- clean :
-- rm -f ${OBJS} core a.out *~ \#* ${EXECUTABLE} ${MAKEFILE}.bak
-+ rm -f ${OBJS} core a.out *~ \#* ${EXECUTABLE} ${MAKEFILE}.bak \
-+ ${BIN}/${EXECUTABLE}
-
-
- ${OBJ} : ${MAKEFILE}
-
- ${EXECUTABLE} : ${OBJS}
-- ${CC} ${OBJS} ${LIBS} -o ${EXECUTABLE}
-+ ${CXX} ${LDFLAGS} ${OBJS} ${LIBS} -o ${EXECUTABLE}
- chmod 755 ${EXECUTABLE}
-
diff --git a/debian/patches/hashbang b/debian/patches/hashbang
deleted file mode 100644
index b4dceab..0000000
--- a/debian/patches/hashbang
+++ /dev/null
@@ -1,43 +0,0 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Description: add #! lines as needed
---- trinityrnaseq.orig/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh
-+++ trinityrnaseq/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
- ../../../Chrysalis/GraphFromFasta -i inchworm.K25.L25.fa -r both.fa -min_contig_length 100 -min_glue 0 -glue_factor 0 -min_iso_ratio 0 -t 4 -k 24 -kk 48
---- trinityrnaseq.orig/sample_data/test_GOSeq_trinotate_pipe/Spombe/runMe.sh
-+++ trinityrnaseq/sample_data/test_GOSeq_trinotate_pipe/Spombe/runMe.sh
-@@ -1,3 +1,4 @@
-+#!/bin/sh
- ../../../Analysis/DifferentialExpression/run_GOseq.pl --factor_labeling hs_induced_vs_log.factors --GO_assignments Trinotate_report.xls.trans.gene_ontology --lengths Trinity.seq_lengths
-
- ../../../Analysis/DifferentialExpression/run_GOseq.pl --factor_labeling ds_induced_vs_log.factors --GO_assignments Trinotate_report.xls.trans.gene_ontology --lengths Trinity.seq_lengths
---- trinityrnaseq.orig/sample_data/test_Inchworm/runMe_MPI.sh
-+++ trinityrnaseq/sample_data/test_Inchworm/runMe_MPI.sh
-@@ -1,3 +1,4 @@
-+#!/bin/sh
- if [ ! -e jellyfish.kmers.fa ]; then
- gunzip -c jellyfish.kmers.fa.gz > jellyfish.kmers.fa
- fi
---- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh
-+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh
-@@ -1 +1,2 @@
--/home/unix/bhaas/SVN/trinityrnaseq/trunk/util/bowtie_PE_separate_then_join.pl --seqType fq --left ../reads.left.fq --right ../reads.right.fq --target refSeqs.fa --aligner bowtie -- -p 4 --all --best --strata -m 300
-+#!/bin/bash
-+/usr/lib/trinityrnaseq/util/bowtie_PE_separate_then_join.pl --seqType fq --left ../reads.left.fq --right ../reads.right.fq --target refSeqs.fa --aligner bowtie -- -p 4 --all --best --strata -m 300
---- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh
-+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
- ../../../../Trinity.pl --seqType fq --left clean.left.fq --right clean.right.fq --seqType fq --JM 1G --bfly_opts "-V 15 --stderr "
---- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh
-+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh
-@@ -1 +1,2 @@
-+#!/bin/sh
- ../../../../Trinity.pl --seqType fq --left ex5.reads.left.fq --right ex5.reads.right.fq --seqType fq --JM 1G --bfly_opts "-V 15 --stderr"
---- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh
-+++ trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh
-@@ -1,2 +1,3 @@
-+#!/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
-
diff --git a/debian/patches/noExitTester b/debian/patches/noExitTester
index 123ba06..793ee09 100644
--- a/debian/patches/noExitTester
+++ b/debian/patches/noExitTester
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Don't try to test Java
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -2260,32 +2260,6 @@
+@@ -2283,32 +2283,6 @@
die "Error, cannot find 'java'. Please be sure it is available within your \${PATH} setting and then try again.";
}
diff --git a/debian/patches/reproducible-build b/debian/patches/reproducible-build
deleted file mode 100644
index ffa0ca0..0000000
--- a/debian/patches/reproducible-build
+++ /dev/null
@@ -1,22 +0,0 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Description: Allow overriding of the MAKE_DATE define
-Enables reproducible builds
---- trinityrnaseq.orig/Chrysalis/Makefile
-+++ trinityrnaseq/Chrysalis/Makefile
-@@ -52,6 +52,7 @@
- ##############################################################################
-
- DATE = $(shell date)
-+BUILD_DATETIME ?= $(DATE) # allow for overrides to enable reproducible builds
- OS_NAME = $(shell uname -s)
- NODE_NAME = $(shell uname -n)
- OS_RELEASE = $(shell uname -r)
-@@ -277,7 +278,7 @@
-
- # Base definitions:
- SYS_DEFS = \
-- -DMAKE_DATE='"$(DATE)"' \
-+ -DMAKE_DATE='"$(BUILD_DATETIME)"' \
- -DMAKE_OS_RELEASE='"$(OS_RELEASE)"' \
- -DMAKE_RELEASE='"$(RELEASE)"' \
- -DNEW_MAKEFILE
diff --git a/debian/patches/scaffold_iworm_contigs-Makefile-fix-clean b/debian/patches/scaffold_iworm_contigs-Makefile-fix-clean
deleted file mode 100644
index b966e01..0000000
--- a/debian/patches/scaffold_iworm_contigs-Makefile-fix-clean
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Description: removes link to zlib; add hardening flags; makes clean target
-resiliant
---- trinityrnaseq.orig/trinity-plugins/scaffold_iworm_contigs/Makefile
-+++ trinityrnaseq/trinity-plugins/scaffold_iworm_contigs/Makefile
-@@ -2,9 +2,9 @@
- prefix = ../htslib
-
- ScaffoldIwormContigs:
-- $(CXX) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -lz -o scaffold_iworm_contigs
-+ $(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
-
- clean:
-- rm scaffold_iworm_contigs
-+ rm -f scaffold_iworm_contigs
-
-
diff --git a/debian/patches/series b/debian/patches/series
index 7772cf5..479b088 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,15 +1,9 @@
-spelling
skip-kallisto-deseq2-tests
-hashbang
-chrysalis-make-tweak
noExitTester
jellyfish-path
update-paths
collections15-to-4
0002-fix_istream_failure_call.patch
fix_system_paths
-hardening
-reproducible-build
-scaffold_iworm_contigs-Makefile-fix-clean
disable-version-check
adjust-trimmomatic-adapters-path
diff --git a/debian/patches/skip-kallisto-deseq2-tests b/debian/patches/skip-kallisto-deseq2-tests
index c01e0e5..68a215e 100644
--- a/debian/patches/skip-kallisto-deseq2-tests
+++ b/debian/patches/skip-kallisto-deseq2-tests
@@ -25,33 +25,5 @@ Debian
+ #../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method ROTS -s samples.txt -o ROTS_outdir --ROTS_B 50 # make it go faster, use more in practice
+ #cd ROTS_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
- clean:
- rm -rf ./edgeR_outdir
---- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/Makefile
-+++ trinityrnaseq/sample_data/test_Trinity_Assembly/Makefile
-@@ -24,7 +24,11 @@
- ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method eXpress --aln_method bowtie2 --trinity_mode --prep_reference --output_dir eXpress_PE
- test_kallisto:
-+ifeq "" "$(shell which kallisto)"
-+ echo skipping kallisto test
-+else
- ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --est_method kallisto --trinity_mode --prep_reference --output_dir kallisto_PE
-+endif
-
- test_bowtie_PE_read_estimates:
- ../../util/bowtie_PE_separate_then_join.pl --seqType fq --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie
---- trinityrnaseq.orig/sample_data/test_align_and_estimate_abundance/Makefile
-+++ trinityrnaseq/sample_data/test_align_and_estimate_abundance/Makefile
-@@ -9,7 +9,11 @@
- ./align_and_estimate_tester.pl eXpress
-
- test_kallisto:
-+ifeq "" "$(shell which kallisto)"
-+ echo skipping kallisto test
-+else
- ./align_and_estimate_tester.pl kallisto
-+endif
-
-
- clean:
+ test_PtR_PCA:
diff --git a/debian/patches/spelling b/debian/patches/spelling
deleted file mode 100644
index 1dcc7f2..0000000
--- a/debian/patches/spelling
+++ /dev/null
@@ -1,35 +0,0 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Description: occurences -> occurrences
---- trinityrnaseq.orig/Inchworm/src/IRKE.cpp
-+++ trinityrnaseq/Inchworm/src/IRKE.cpp
-@@ -93,7 +93,7 @@
- record_counter[i] = 0;
- }
-
-- cerr << "-reading Kmer occurences..." << endl;
-+ cerr << "-reading Kmer occurrences..." << endl;
- start = time(NULL);
-
- Fasta_reader fasta_reader(fasta_filename);
---- trinityrnaseq.orig/Chrysalis/MakeDepend.cc
-+++ trinityrnaseq/Chrysalis/MakeDepend.cc
-@@ -420,7 +420,7 @@
-
- // The vector of pairs count_per_provider[] simply reverses the map
- // provider_counts[], copying each map element B->n to an ordered pair (n,B),
-- // so that the resulting vector can be sorted by number of occurences, rather
-+ // so that the resulting vector can be sorted by number of occurrences, rather
- // than provider name. (Why not build the mapping as a vector in the first
- // place? Efficiency: keeping the vector sorted while building up the map
- // would require a lot of copying of data everytime a new provider name was
---- trinityrnaseq.orig/Inchworm/src/fastaToKmerCoverageStats.cpp
-+++ trinityrnaseq/Inchworm/src/fastaToKmerCoverageStats.cpp
-@@ -168,7 +168,7 @@
- for (int i = 0; i < omp_get_max_threads(); i++) {
- record_counter[i] = 0;
- }
-- cerr << "-reading Kmer occurences..." << endl;
-+ cerr << "-reading Kmer occurrences..." << endl;
- start = time(NULL);
- Fasta_reader fasta_reader(kmers_fasta_file);
- #pragma omp parallel private (myTid)
diff --git a/debian/patches/update-paths b/debian/patches/update-paths
index 1711bfd..58e1da1 100644
--- a/debian/patches/update-paths
+++ b/debian/patches/update-paths
@@ -28,7 +28,7 @@ Last-Updated: 2015-02-22
my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
$ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
-@@ -324,7 +324,7 @@
+@@ -325,7 +325,7 @@
### Butterfly-related options: ####
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
diff --git a/debian/rules b/debian/rules
index f4abc28..19b9b42 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,7 +13,7 @@ LAST_CHANGE := $(shell dpkg-parsechangelog -S Date)
export BUILD_DATETIME := $(shell LC_ALL=C date -u -d '$(LAST_CHANGE)')
DPKG_EXPORT_BUILDFLAGS = 1
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
include /usr/share/dpkg/buildflags.mk
%:
@@ -55,7 +55,6 @@ override_dh_install-arch:
${BASEDIR}/util/support_scripts/trinity_install_tests.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
override_dh_install-indep:
dh_install -i
diff --git a/debian/trinityrnaseq.docs b/debian/trinityrnaseq.docs
index c88e05d..3d4d992 100644
--- a/debian/trinityrnaseq.docs
+++ b/debian/trinityrnaseq.docs
@@ -1,4 +1,3 @@
README
-Release.Notes
debian/tests/run-tests
hpc_conf
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git
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