Author: osallou Date: 2013-02-09 12:02:54 +0000 (Sat, 09 Feb 2013) New Revision: 12970
Added: trunk/packages/soap/soapdenovo2/tags/223-1/ trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog trunk/packages/soap/soapdenovo2/tags/223-1/debian/control trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules Removed: trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog trunk/packages/soap/soapdenovo2/tags/223-1/debian/control trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules Log: [svn-buildpackage] Tagging soapdenovo2 223-1 Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian 2013-02-09 10:56:54 UTC (rev 12964) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian 2013-02-09 12:02:54 UTC (rev 12970) @@ -1,9 +0,0 @@ -* SOAPdenovo2 - -Binaries are soapdenovo2-63mer and soapdenovo2-127mer. -See manpage for further explanations - -SparsePregraph does not compile from source, as such binaries are not provided. - - -- Olivier Sallou <[email protected]> Sat, 09 Feb 2013 10:40:45 +0100 - Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian (from rev 12965, trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,9 @@ +* SOAPdenovo2 + +Binaries are soapdenovo2-63mer and soapdenovo2-127mer. +See manpage soapdenovo2 for further explanations + +SparsePregraph does not compile from source, as such binaries are not provided. + + -- Olivier Sallou <[email protected]> Sat, 09 Feb 2013 10:40:45 +0100 + Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-02-09 10:56:54 UTC (rev 12964) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog 2013-02-09 12:02:54 UTC (rev 12970) @@ -1,5 +0,0 @@ -soapdenovo2 (223-1) UNRELEASED; urgency=low - - * Initial release (Closes: #700160) - - -- Olivier Sallou <[email protected]> Sat, 09 Feb 2013 10:40:45 +0100 Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog (from rev 12967, trunk/packages/soap/soapdenovo2/trunk/debian/changelog) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,5 @@ +soapdenovo2 (223-1) unstable; urgency=low + + * Initial release (Closes: #700160) + + -- Olivier Sallou <[email protected]> Sat, 09 Feb 2013 10:40:45 +0100 Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/control =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-02-09 10:56:54 UTC (rev 12964) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/control 2013-02-09 12:02:54 UTC (rev 12970) @@ -1,24 +0,0 @@ -Source: soapdenovo2 -Section: science -Priority: optional -Build-Depends: debhelper (>= 8),g++ -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Olivier Sallou <[email protected]> -DM-Upload-Allowed: yes -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soapdenovo2/trunk/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/soap/soapdenovo2/ -Standards-Version: 3.9.3 -Homepage: http://soap.genomics.org.cn/soapdenovo.html - -Package: soapdenovo2 -Architecture: any-amd64 any-ppc64 any-ia64 -#Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Description: short-read assembly method to build de novo draft assembly - SOAPdenovo is a novel short-read assembly method that can build a de novo draft - assembly for the human-sized genomes. The program is specially designed to - assemble Illumina GA short reads. - . - It creates new opportunities for building reference - sequences and carrying out accurate analyses of unexplored genomes in a cost - effective way. Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/control (from rev 12968, trunk/packages/soap/soapdenovo2/trunk/debian/control) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/control (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/control 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,24 @@ +Source: soapdenovo2 +Section: science +Priority: optional +Build-Depends: debhelper (>= 8), hardening-includes +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +DM-Upload-Allowed: yes +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soapdenovo2/trunk/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/soap/soapdenovo2/ +Standards-Version: 3.9.3 +Homepage: http://soap.genomics.org.cn/soapdenovo.html + +Package: soapdenovo2 +Architecture: any-amd64 any-ppc64 any-ia64 +#Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: short-read assembly method to build de novo draft assembly + SOAPdenovo is a novel short-read assembly method that can build a de novo draft + assembly for the human-sized genomes. The program is specially designed to + assemble Illumina GA short reads. + . + It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost + effective way. Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening (from rev 12969, trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,30 @@ +Subject: add fortify flags +Description: Makefile does not load CFLAGS + from env, add extra flags for debian fortify +Forwarded: no +Author: Olivier Sallou <[email protected]> +Last-Updated: 2013-02-09 +--- a/standardPregraph/Makefile ++++ b/standardPregraph/Makefile +@@ -8,7 +8,11 @@ + CC= gcc #gcc + GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) + GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) +-CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 ++CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 ++CFLAGS += `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` ++CFLAGS+=$(HARDENING_CFLAGS) ++LDFLAGS = `dpkg-buildflags --get LDFLAGS` ++LDFLAGS+=$(HARDENING_LDFLAGS) + DFLAGS= + OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \ + concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \ +@@ -81,7 +85,7 @@ + + SOAPdenovo: envTest $(OBJS) + @printf "Linking... \r" +- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) ++ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) + @printf "$(PROG) compilation done.\n"; + + clean: Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path 2013-02-09 10:56:54 UTC (rev 12964) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path 2013-02-09 12:02:54 UTC (rev 12970) @@ -1,36 +0,0 @@ ---- a/sparsePregraph/Makefile -+++ b/sparsePregraph/Makefile -@@ -1,11 +1,11 @@ --CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc -+CC= gcc #gcc - CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 - DFLAGS= - OBJS= build_graph.o build_edge.o multi_threads.o \ - build_preArc.o pregraph_sparse.o io_func.o\ - global.o convert_soapdenovo.o - PROG= --INCLUDES= -I./inc -+INCLUDES= -I./inc - SUBDIRS= . - LIBPATH= -L/usr/lib64 - LIBS= -pthread -lz -lstdc++ -L./inc ---- a/standardPregraph/Makefile -+++ b/standardPregraph/Makefile -@@ -5,7 +5,7 @@ - # - ################################### - --CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc -+CC= gcc #gcc - GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) - GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) - CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 -@@ -78,8 +78,6 @@ - - envTest: - @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;' -- @test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' -- @test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' - - SOAPdenovo: envTest $(OBJS) - @printf "Linking... \r" Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path (from rev 12965, trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,41 @@ +Subject: gcc wrong hard coded path +Description: remove path for gcc +Forwarded: yes +Author: Olivier Sallou <[email protected]> +Last-Updated: 2013-02-09 +--- a/sparsePregraph/Makefile ++++ b/sparsePregraph/Makefile +@@ -1,11 +1,11 @@ +-CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc ++CC= gcc #gcc + CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 + DFLAGS= + OBJS= build_graph.o build_edge.o multi_threads.o \ + build_preArc.o pregraph_sparse.o io_func.o\ + global.o convert_soapdenovo.o + PROG= +-INCLUDES= -I./inc ++INCLUDES= -I./inc + SUBDIRS= . + LIBPATH= -L/usr/lib64 + LIBS= -pthread -lz -lstdc++ -L./inc +--- a/standardPregraph/Makefile ++++ b/standardPregraph/Makefile +@@ -5,7 +5,7 @@ + # + ################################### + +-CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc ++CC= gcc #gcc + GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) + GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) + CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 +@@ -78,8 +78,6 @@ + + envTest: + @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;' +- @test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' +- @test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' + + SOAPdenovo: envTest $(OBJS) + @printf "Linking... \r" Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name 2013-02-09 10:56:54 UTC (rev 12964) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name 2013-02-09 12:02:54 UTC (rev 12970) @@ -1,11 +0,0 @@ ---- a/standardPregraph/main.c -+++ b/standardPregraph/main.c -@@ -99,7 +99,7 @@ - - static void display_usage () - { -- fprintf ( stderr, "\nUsage: SOAPdenovo <command> [option]\n" ); -+ fprintf ( stderr, "\nUsage: soapdenovo2-63mer/soapdenovo2-127mer <command> [option]\n" ); - fprintf ( stderr, " pregraph construct kmer-graph\n" ); - fprintf ( stderr, " contig eliminate errors and output contigs\n" ); - fprintf ( stderr, " map map reads to contigs\n" ); Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name (from rev 12965, trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,18 @@ +Subject: update binary name +Description: usage show SOAPdenovo binary name + while generated binaries are kmer dependent. + Debian modification to lowercase applied too. +Forwarded: no +Author: Olivier Sallou <[email protected]> +Last-Updated: 2013-02-09 +--- a/standardPregraph/main.c ++++ b/standardPregraph/main.c +@@ -99,7 +99,7 @@ + + static void display_usage () + { +- fprintf ( stderr, "\nUsage: SOAPdenovo <command> [option]\n" ); ++ fprintf ( stderr, "\nUsage: soapdenovo2-63mer/soapdenovo2-127mer <command> [option]\n" ); + fprintf ( stderr, " pregraph construct kmer-graph\n" ); + fprintf ( stderr, " contig eliminate errors and output contigs\n" ); + fprintf ( stderr, " map map reads to contigs\n" ); Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-02-09 10:56:54 UTC (rev 12964) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series 2013-02-09 12:02:54 UTC (rev 12970) @@ -1,2 +0,0 @@ -fix_gcc_path -fix_usage_name Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series (from rev 12967, trunk/packages/soap/soapdenovo2/trunk/debian/patches/series) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,3 @@ +fix_gcc_path +fix_usage_name +add_hardening Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-02-09 10:56:54 UTC (rev 12964) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules 2013-02-09 12:02:54 UTC (rev 12970) @@ -1,23 +0,0 @@ -#!/usr/bin/make -f -# -*- makefile -*- - -# Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 - -%: - dh $@ - -override_dh_auto_build: - cd standardPregraph && make 63mer=1 - cd standardPregraph && make 127mer=1 -# cd sparsePregraph && make - dh_auto_build - -override_dh_install: - dh_install - cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP* - -override_dh_clean: - cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean - cd sparsePregraph && make clean - dh_clean Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules (from rev 12967, trunk/packages/soap/soapdenovo2/trunk/debian/rules) =================================================================== --- trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules (rev 0) +++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules 2013-02-09 12:02:54 UTC (rev 12970) @@ -0,0 +1,34 @@ +#!/usr/bin/make -f +# -*- makefile -*- +export DEB_BUILD_HARDENING=1 +export DEB_BUILD_HARDENING_FORTIFY=1 + +include /usr/share/hardening-includes/hardening.make + +CFLAGS=$(shell dpkg-buildflags --get CFLAGS) +LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) +CFLAGS+=$(HARDENING_CFLAGS) +CXXFLAGS+=$(HARDENING_CXXFLAGS) +LDFLAGS+=$(HARDENING_LDFLAGS) + + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ + +override_dh_auto_build: + cd standardPregraph && make 63mer=1 + cd standardPregraph && make 127mer=1 +# cd sparsePregraph && make + dh_auto_build + +override_dh_install: + dh_install + cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP* + +override_dh_clean: + cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean + cd sparsePregraph && make clean + dh_clean _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
