[med-svn] [freebayes] 02/02: Use Debian packaged bamtools; TODO: Package https://github.com/ekg/vcflib
Andreas Tille
tille at debian.org
Wed May 28 19:25:26 UTC 2014
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 <tille at debian.org>
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 <chapmanb at 50mail.com> Sun, 02 Feb 2014 05:14:33 -0500
+ -- Andreas Tille <tille at debian.org> 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 <chapmanb at 50mail.com>
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 $(BAMTOOLS_ROOT)/build && make clean)
- cd ../vcflib/smithwaterman && make clean
-
diff --git a/debian/patches/series b/debian/patches/series
index 5df678c..58f3dd9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1 @@
-clean.patch
+use_debian_packaged_bamtools.patch
diff --git a/debian/patches/use_debian_packaged_bamtools.patch b/debian/patches/use_debian_packaged_bamtools.patch
new file mode 100644
index 0000000..068db14
--- /dev/null
+++ b/debian/patches/use_debian_packaged_bamtools.patch
@@ -0,0 +1,89 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 28 May 2014 21:23:38 +0200
+Description: Use Debian packaged bamtools
+
+--- freebayes.orig/src/Makefile
++++ freebayes/src/Makefile
+@@ -12,11 +12,10 @@
+ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64
+ #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+
+-BAMTOOLS_ROOT=../bamtools
+ VCFLIB_ROOT=../vcflib
+
+-LIBS = -L./ -L$(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
+
--
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