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commit 11fefd4359dd64a75f094b7ce8d31fa92d7cdb6b Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> - ---- - -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 <[email protected]> Description: Disable the version "phone home" for privacy --- trinityrnaseq.orig/Trinity +++ trinityrnaseq/Trinity -@@ -552,7 +552,7 @@ +@@ -553,7 +553,7 @@ my $ANANAS_DIR = ""; diff --git a/debian/patches/fix_system_paths b/debian/patches/fix_system_paths index fb7780e..e5a7712 100644 --- a/debian/patches/fix_system_paths +++ b/debian/patches/fix_system_paths @@ -6,7 +6,7 @@ Author: Tim Booth <[email protected]> use FindBin; use File::Basename; --$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 <[email protected]> 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 <[email protected]> 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 <[email protected]> ---- 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 <[email protected]> -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 <[email protected]> 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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
