diff options
| -rw-r--r-- | .SRCINFO | 20 | ||||
| -rw-r--r-- | PKGBUILD | 47 | ||||
| -rw-r--r-- | bcftools-profile.sh | 1 | ||||
| -rw-r--r-- | makefile-system-htslib.patch | 78 |
4 files changed, 146 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..672799cc63a0 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,20 @@ +pkgbase = bcftools + pkgdesc = Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants + pkgver = 1.2 + pkgrel = 3 + url = http://samtools.github.io/bcftools/ + arch = i686 + arch = x86_64 + license = GPL + depends = gsl + depends = htslib + depends = perl + source = bcftools-1.2.tar.gz::https://github.com/samtools/bcftools/archive/1.2.tar.gz + source = bcftools-profile.sh + source = makefile-system-htslib.patch + md5sums = 87efbd0092b6e4828c17842c9ae57ec9 + md5sums = 50efd8fdb3f4c11a5dff7748c666d90e + md5sums = 5ae8f6433b42acf1f4bc7b7658a10805 + +pkgname = bcftools + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..3327eeea3a3e --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,47 @@ +# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> + +pkgname=bcftools +pkgver=1.2 +pkgrel=3 +pkgdesc="Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants" +arch=('i686' 'x86_64') +url="http://samtools.github.io/bcftools/" +license=('GPL') +depends=('gsl' 'htslib' 'perl') +source=($pkgname-$pkgver.tar.gz::https://github.com/samtools/bcftools/archive/$pkgver.tar.gz + bcftools-profile.sh + makefile-system-htslib.patch) +md5sums=('87efbd0092b6e4828c17842c9ae57ec9' + '50efd8fdb3f4c11a5dff7748c666d90e' + '5ae8f6433b42acf1f4bc7b7658a10805') + +prepare() { + cd $srcdir/$pkgname-$pkgver + + # patch Makefile to make it work with a system-provided htslib + patch -Np1 -i $srcdir/makefile-system-htslib.patch +} + +build() { + cd $srcdir/$pkgname-$pkgver + + make USE_GPL=1 +} + +check() { + cd $srcdir/$pkgname-$pkgver + + make USE_GPL=1 test +} + +package() { + cd $srcdir/$pkgname-$pkgver + + make USE_GPL=1 DESTDIR=$pkgdir prefix=/usr install + + for plugin in plugins/*.so ; do + install -Dm755 $plugin $pkgdir/usr/lib/bcftools/$(basename $plugin) + done + + install -Dm644 $srcdir/bcftools-profile.sh $pkgdir/etc/profile.d/bcftools.sh +} diff --git a/bcftools-profile.sh b/bcftools-profile.sh new file mode 100644 index 000000000000..c31d0ed39cbc --- /dev/null +++ b/bcftools-profile.sh @@ -0,0 +1 @@ +export BCFTOOLS_PLUGINS=/usr/lib/bcftools diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch new file mode 100644 index 000000000000..737ab0d61d5d --- /dev/null +++ b/makefile-system-htslib.patch @@ -0,0 +1,78 @@ +diff -aur bcftools-1.2/Makefile bcftools-1.2-patched/Makefile +--- bcftools-1.2/Makefile 2015-02-02 16:40:17.000000000 +0100 ++++ bcftools-1.2-patched/Makefile 2015-02-04 12:33:10.627010914 +0100 +@@ -29,11 +29,9 @@ + all: $(PROG) $(TEST_PROG) + + # Adjust $(HTSDIR) to point to your top-level htslib directory +-HTSDIR = ../htslib +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++HTSDIR = /usr/include ++BGZIP = bgzip ++TABIX = tabix + + CC = gcc + CFLAGS = -g -Wall -Wc++-compat -O2 +@@ -52,7 +50,7 @@ + ifdef USE_GPL + CFLAGS += -DUSE_GPL + OBJS += polysomy.o +- LDLIBS = -lgsl -lcblas ++ LDLIBS = -lgsl -lgslcblas + endif + + prefix = /usr/local +@@ -90,10 +88,10 @@ + .c.o: + $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ + +-test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX) ++test: $(PROG) plugins test/test-rbuf + ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) + +-test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX) ++test-plugins: $(PROG) plugins test/test-rbuf + ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) + + +@@ -102,8 +100,8 @@ + PLUGINS = $(PLUGINC:.c=.so) + PLUGINM = $(PLUGINC:.c=.mk) + +-%.so: %.c version.h version.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts ++%.so: %.c version.h version.c ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -lhts + + -include $(PLUGINM) + +@@ -158,8 +156,8 @@ + test/test-rbuf: test/test-rbuf.o + $(CC) $(CFLAGS) -o $@ -lm -ldl $< + +-bcftools: $(HTSLIB) $(OBJS) +- $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS) ++bcftools: $(OBJS) ++ $(CC) $(CFLAGS) -o $@ $(OBJS) -lpthread -lz -lm -ldl -lhts $(LDLIBS) + + doc/bcftools.1: doc/bcftools.txt + cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt +diff -aur bcftools-1.2/plugins/fixploidy.mk bcftools-1.2-patched/plugins/fixploidy.mk +--- bcftools-1.2/plugins/fixploidy.mk 2015-02-02 16:40:17.000000000 +0100 ++++ bcftools-1.2-patched/plugins/fixploidy.mk 2015-02-04 12:23:15.376535358 +0100 +@@ -1,2 +1,2 @@ +-plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts ++plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts +diff -aur bcftools-1.2/plugins/vcf2sex.mk bcftools-1.2-patched/plugins/vcf2sex.mk +--- bcftools-1.2/plugins/vcf2sex.mk 2015-02-02 16:40:17.000000000 +0100 ++++ bcftools-1.2-patched/plugins/vcf2sex.mk 2015-02-04 12:25:51.240884001 +0100 +@@ -1,2 +1,2 @@ +-plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts ++plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts |