This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository freebayes.
commit e7e5c2e3d55fe3cb436289dd1a91cfd5dd613046 Author: Andreas Tille <[email protected]> Date: Wed May 28 21:25:01 2014 +0200 Use Debian packaged bamtools; TODO: Package https://github.com/ekg/vcflib --- debian/changelog | 3 +- debian/control | 3 +- debian/patches/clean.patch | 10 --- debian/patches/series | 2 +- debian/patches/use_debian_packaged_bamtools.patch | 89 +++++++++++++++++++++++ 5 files changed, 94 insertions(+), 13 deletions(-) diff --git a/debian/changelog b/debian/changelog index 56c5ecd..064263a 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,6 @@ freebayes (0.9.14+dfsg-1) UNRELEASED; urgency=low + TODO: Package https://github.com/ekg/vcflib * Initial FreeBayes packaging (Closes: #nnnn) - -- Brad Chapman <[email protected]> Sun, 02 Feb 2014 05:14:33 -0500 + -- Andreas Tille <[email protected]> Wed, 28 May 2014 21:23:38 +0200 diff --git a/debian/control b/debian/control index 41b54e7..329b960 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,8 @@ Priority: optional Maintainer: Brad Chapman <[email protected]> Build-Depends: debhelper (>= 9), cmake (>= 2), - zlib1g-dev + zlib1g-dev, + libbamtools-dev Standards-Version: 3.9.5 Homepage: https://github.com/ekg/freebayes Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/freebayes.git diff --git a/debian/patches/clean.patch b/debian/patches/clean.patch deleted file mode 100644 index 34aefeb..0000000 --- a/debian/patches/clean.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- freebayes.orig/src/Makefile -+++ freebayes/src/Makefile -@@ -259,6 +259,6 @@ - - clean: - rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} -- cd $(BAMTOOLS_ROOT)/build && make clean -+ test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean) - cd ../vcflib/smithwaterman && make clean - diff --git a/debian/patches/series b/debian/patches/series index 5df678c..58f3dd9 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1 @@ -clean.patch +use_debian_packaged_bamtools.patch diff --git a/debian/patches/use_debian_packaged_bamtools.patch b/debian/patches/use_debian_packaged_bamtools.patch new file mode 100644 index 0000000..068db14 --- /dev/null +++ b/debian/patches/use_debian_packaged_bamtools.patch @@ -0,0 +1,89 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Wed, 28 May 2014 21:23:38 +0200 +Description: Use Debian packaged bamtools + +--- freebayes.orig/src/Makefile ++++ freebayes/src/Makefile +@@ -12,11 +12,10 @@ + CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 + #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2 + +-BAMTOOLS_ROOT=../bamtools + VCFLIB_ROOT=../vcflib + +-LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz -lm +-INCLUDE = -I$(BAMTOOLS_ROOT)/src -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/ ++LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabix -lz -lm ++INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/ + + all: autoversion ../bin/freebayes ../bin/bamleftalign + +@@ -34,10 +33,6 @@ + + .PHONY: all static debug profiling gprof + +-# builds bamtools static lib, and copies into root +-$(BAMTOOLS_ROOT)/lib/libbamtools.a: +- cd $(BAMTOOLS_ROOT) && mkdir -p build && cd build && cmake .. && $(MAKE) +- + + OBJECTS=BedReader.o \ + CNV.o \ +@@ -69,8 +64,7 @@ + ../vcflib/smithwaterman/LeftAlign.o \ + ../vcflib/smithwaterman/Repeats.o \ + ../vcflib/smithwaterman/IndelAllele.o \ +- Variant.o \ +- $(BAMTOOLS_ROOT)/lib/libbamtools.a ++ Variant.o + + HEADERS=multichoose.h version_git.h + +@@ -85,10 +79,10 @@ + dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) + $(CC) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS) + +-bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o +- $(CC) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a -o ../bin/bamleftalign $(LIBS) ++bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o ++ $(CC) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS) + +-bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamfiltertech.o $(OBJECTS) $(HEADERS) ++bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS) + $(CC) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS) + + +@@ -103,7 +97,7 @@ + dummy.o: dummy.cpp AlleleParser.o Allele.o + $(CC) $(CFLAGS) $(INCLUDE) -c dummy.cpp + +-freebayes.o: freebayes.cpp TryCatch.h $(BAMTOOLS_ROOT)/lib/libbamtools.a ++freebayes.o: freebayes.cpp TryCatch.h + $(CC) $(CFLAGS) $(INCLUDE) -c freebayes.cpp + + fastlz.o: fastlz.c fastlz.h +@@ -124,7 +118,7 @@ + Ewens.o: Ewens.cpp Ewens.h + $(CC) $(CFLAGS) $(INCLUDE) -c Ewens.cpp + +-AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a ++AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h + $(CC) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp + + Utility.o: Utility.cpp Utility.h Sum.h Product.h +@@ -169,7 +163,7 @@ + bamfiltertech.o: bamfiltertech.cpp + $(CC) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp + +-LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a ++LeftAlign.o: LeftAlign.h LeftAlign.cpp + $(CC) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp + + IndelAllele.o: IndelAllele.cpp IndelAllele.h +@@ -259,6 +253,5 @@ + + clean: + rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} +- test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean) + cd ../vcflib/smithwaterman && make clean + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
