diff options
| -rw-r--r-- | .SRCINFO | 10 | ||||
| -rw-r--r-- | PKGBUILD | 24 | ||||
| -rw-r--r-- | makefile-system-htslib.patch | 87 |
3 files changed, 17 insertions, 104 deletions
@@ -1,8 +1,8 @@ # Generated by mksrcinfo v8 -# Sun May 14 21:02:41 UTC 2017 +# Wed Jun 28 15:26:46 UTC 2017 pkgbase = bcftools pkgdesc = Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants - pkgver = 1.4.1 + pkgver = 1.5 pkgrel = 1 url = http://samtools.github.io/bcftools/ arch = i686 @@ -11,10 +11,8 @@ pkgbase = bcftools depends = gsl depends = htslib optdepends = python2: needed for some scripts - source = https://github.com/samtools/bcftools/releases/download/1.4.1/bcftools-1.4.1.tar.bz2 - source = makefile-system-htslib.patch - md5sums = 103729569ca3e265b13d2fed5775016e - md5sums = 1777e7d3bcfd428de407f62c870904cb + source = https://github.com/samtools/bcftools/releases/download/1.5/bcftools-1.5.tar.bz2 + md5sums = e43efe3df5f9c55acb4b48cee214d281 pkgname = bcftools @@ -1,7 +1,7 @@ # Maintainer: Christian Krause ("wookietreiber") <christian.krause@mailbox.org> pkgname=bcftools -pkgver=1.4.1 +pkgver=1.5 pkgrel=1 pkgdesc="Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants" arch=('i686' 'x86_64') @@ -9,8 +9,7 @@ url="http://samtools.github.io/bcftools/" license=('GPL') depends=('gsl' 'htslib') optdepends=('python2: needed for some scripts') -source=(https://github.com/samtools/bcftools/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2 - makefile-system-htslib.patch) +source=(https://github.com/samtools/bcftools/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2) prepare() { cd $srcdir/$pkgname-$pkgver @@ -21,28 +20,31 @@ prepare() { sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ -e 's|#!/usr/bin/python|#!/usr/bin/env python2|' \ -i misc/plot-roh.py misc/guess-ploidy.py - - # patch Makefile to make it work with a system-provided htslib - patch -i $srcdir/makefile-system-htslib.patch } build() { cd $srcdir/$pkgname-$pkgver - make prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 + ./configure \ + --prefix=/usr \ + --enable-libgsl \ + --with-bcf-plugin-dir=/usr/lib/$pkgname \ + --with-cblas=gslcblas \ + --with-htslib=system + + make } check() { cd $srcdir/$pkgname-$pkgver - make prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 test + make check } package() { cd $srcdir/$pkgname-$pkgver - make prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 DESTDIR=$pkgdir install + make DESTDIR=$pkgdir install } -md5sums=('103729569ca3e265b13d2fed5775016e' - '1777e7d3bcfd428de407f62c870904cb') +md5sums=('e43efe3df5f9c55acb4b48cee214d281') diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch deleted file mode 100644 index 7e98ae5d9f98..000000000000 --- a/makefile-system-htslib.patch +++ /dev/null @@ -1,87 +0,0 @@ ---- Makefile.orig 2017-03-14 07:26:49.191430557 +0100 -+++ Makefile 2017-03-14 07:27:44.929678345 +0100 -@@ -29,20 +29,10 @@ - all: $(PROG) $(TEST_PROG) - - # Adjust $(HTSDIR) to point to your top-level htslib directory --HTSDIR = htslib-1.4.1 --include $(HTSDIR)/htslib.mk --include $(HTSDIR)/htslib_static.mk --HTSLIB = $(HTSDIR)/libhts.a --BGZIP = $(HTSDIR)/bgzip --TABIX = $(HTSDIR)/tabix --HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) --HTSLIB_LIBS = $(HTSLIB_static_LIBS) -+HTSDIR = /usr/include - - CC = gcc --CPPFLAGS = --CFLAGS = -g -Wall -Wc++-compat -O2 --LDFLAGS = --LIBS = -+CFLAGS := -g -Wall -Wc++-compat -O2 $(CFLAGS) - - ifeq "$(shell uname -s)" "Darwin" - DYNAMIC_FLAGS = -Wl,-export_dynamic -@@ -51,8 +41,8 @@ - endif - - # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally --ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) --ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS) -+ALL_CPPFLAGS = -I. $(CPPFLAGS) -+ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(LDFLAGS) - ALL_LIBS = -lm -lz -ldl $(LIBS) - - OBJS = main.o vcfindex.o tabix.o \ -@@ -64,7 +54,7 @@ - mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ - ccall.o em.o prob1.o kmin.o # the original samtools calling - --EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\" -+EXTRA_CPPFLAGS = -I. -DPLUGINPATH=\"$(pluginpath)\" - GSL_LIBS = - - # The polysomy command is not compiled by default because it brings dependency -@@ -73,7 +63,7 @@ - ifdef USE_GPL - EXTRA_CPPFLAGS += -DUSE_GPL - OBJS += polysomy.o peakfit.o -- GSL_LIBS = -lgsl -lcblas -+ GSL_LIBS = -lgsl -lgslcblas - endif - - prefix = /usr/local -@@ -117,12 +107,12 @@ - .c.o: - $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - --test: $(PROG) plugins test/test-rbuf test/test-regidx $(BGZIP) $(TABIX) -+test: $(PROG) plugins test/test-rbuf test/test-regidx - ./test/test-regidx -- ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) -+ ./test/test.pl --exec bgzip=bgzip --exec tabix=tabix - --test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX) -- ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) -+test-plugins: $(PROG) plugins test/test-rbuf -+ ./test/test.pl --plugins --exec bgzip=bgzip --exec tabix=tabix - - - # Plugin rules -@@ -208,11 +198,11 @@ - - test/test-regidx.o: test/test-regidx.c regidx.h - --test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) -- $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS) -+test/test-regidx: test/test-regidx.o regidx.o -+ $(CC) $(ALL_LDFLAGS) -o $@ $^ -lpthread -lhts $(ALL_LIBS) - --bcftools: $(HTSLIB) $(OBJS) -- $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS) -+bcftools: $(OBJS) -+ $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) -lpthread -lhts $(GSL_LIBS) $(ALL_LIBS) - - doc/bcftools.1: doc/bcftools.txt - cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt |