diff options
author | Christian Krause | 2016-01-10 11:44:28 +0100 |
---|---|---|
committer | Christian Krause | 2016-01-10 11:44:28 +0100 |
commit | ce0e65b4a554c65329bc40d6de30120fda1aa0ea (patch) | |
tree | 35760f062f5f98cd24d74bcce1f4430b3eb4be41 | |
parent | 1c012681f904e3b3f380cb3eaefe5730f2357d8c (diff) | |
download | aur-ce0e65b4a554c65329bc40d6de30120fda1aa0ea.tar.gz |
bcftools-1.3-1
-rw-r--r-- | .SRCINFO | 14 | ||||
-rw-r--r-- | PKGBUILD | 29 | ||||
-rw-r--r-- | bcftools-profile.sh | 1 | ||||
-rw-r--r-- | makefile-system-htslib.patch | 136 |
4 files changed, 107 insertions, 73 deletions
@@ -1,7 +1,9 @@ +# Generated by mksrcinfo v8 +# Sun Jan 10 10:43:34 UTC 2016 pkgbase = bcftools pkgdesc = Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants - pkgver = 1.2 - pkgrel = 3 + pkgver = 1.3 + pkgrel = 1 url = http://samtools.github.io/bcftools/ arch = i686 arch = x86_64 @@ -9,12 +11,10 @@ pkgbase = bcftools 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 = https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2 source = makefile-system-htslib.patch - md5sums = 87efbd0092b6e4828c17842c9ae57ec9 - md5sums = 50efd8fdb3f4c11a5dff7748c666d90e - md5sums = 5ae8f6433b42acf1f4bc7b7658a10805 + md5sums = 17f1f7d9e4a03d64a114b43ca896899f + md5sums = 697d169f4a729c0fc61720490b60ea5e pkgname = bcftools @@ -1,47 +1,42 @@ # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> pkgname=bcftools -pkgver=1.2 -pkgrel=3 +pkgver=1.3 +pkgrel=1 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/$pkgver.tar.gz - bcftools-profile.sh +source=(https://github.com/samtools/$pkgname/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2 makefile-system-htslib.patch) -md5sums=('87efbd0092b6e4828c17842c9ae57ec9' - '50efd8fdb3f4c11a5dff7748c666d90e' - '5ae8f6433b42acf1f4bc7b7658a10805') +md5sums=('17f1f7d9e4a03d64a114b43ca896899f' + '697d169f4a729c0fc61720490b60ea5e') prepare() { cd $srcdir/$pkgname-$pkgver + # prevent shipped htslib to be used + rm -rf htslib-1.3 + # patch Makefile to make it work with a system-provided htslib - patch -Np1 -i $srcdir/makefile-system-htslib.patch + patch -i $srcdir/makefile-system-htslib.patch } build() { cd $srcdir/$pkgname-$pkgver - make USE_GPL=1 + make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 } check() { cd $srcdir/$pkgname-$pkgver - make USE_GPL=1 test + make -e prefix=/usr plugindir=/usr/lib/$pkgname 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 $pkgdir/etc/profile.d/bcftools.sh + make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 DESTDIR=$pkgdir install } diff --git a/bcftools-profile.sh b/bcftools-profile.sh deleted file mode 100644 index c31d0ed39cbc..000000000000 --- a/bcftools-profile.sh +++ /dev/null @@ -1 +0,0 @@ -export BCFTOOLS_PLUGINS=/usr/lib/bcftools diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch index 737ab0d61d5d..9965be1135d7 100644 --- a/makefile-system-htslib.patch +++ b/makefile-system-htslib.patch @@ -1,78 +1,118 @@ -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 @@ +--- Makefile.orig 2016-01-10 11:15:35.126733492 +0100 ++++ Makefile 2016-01-10 11:21:31.034859116 +0100 +@@ -28,13 +28,6 @@ + all: $(PROG) $(TEST_PROG) - # Adjust $(HTSDIR) to point to your top-level htslib directory --HTSDIR = ../htslib +-# Adjust $(HTSDIR) to point to your top-level htslib directory +-HTSDIR = htslib-1.3 -include $(HTSDIR)/htslib.mk -HTSLIB = $(HTSDIR)/libhts.a -BGZIP = $(HTSDIR)/bgzip -TABIX = $(HTSDIR)/tabix -+HTSDIR = /usr/include -+BGZIP = bgzip -+TABIX = tabix - +- CC = gcc + CPPFLAGS = CFLAGS = -g -Wall -Wc++-compat -O2 -@@ -52,7 +50,7 @@ +@@ -48,7 +41,7 @@ + vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling + +-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\" ++EXTRA_CPPFLAGS = -I. -DPLUGINPATH=\"$(pluginpath)\" + GSL_LIBS = + + # The polysomy command is not compiled by default because it brings dependency +@@ -57,7 +50,7 @@ ifdef USE_GPL - CFLAGS += -DUSE_GPL - OBJS += polysomy.o -- LDLIBS = -lgsl -lcblas -+ LDLIBS = -lgsl -lgslcblas + EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS = -lgsl -lcblas ++ GSL_LIBS = -lgsl -lgslcblas endif prefix = /usr/local -@@ -90,10 +88,10 @@ +@@ -101,11 +94,11 @@ .c.o: - $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ + $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $< -test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX) +- ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) +test: $(PROG) plugins test/test-rbuf - ./test/test.pl --exec bgzip=$(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) - ++ ./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 + # Plugin rules +@@ -136,20 +129,20 @@ + filter_h = filter.h $(htslib_vcf_h) + ploidy_h = ploidy.h $(htslib_regidx_h) + prob1_h = prob1.h $(htslib_vcf_h) $(call_h) +-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) + cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) - -include $(PLUGINM) + main.o: main.c $(htslib_hts_h) version.h $(bcftools_h) +-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h) +-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) +-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) vcmp.h $(filter_h) ++vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) vcmp.h $(filter_h) ++vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) ++vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) + vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) + vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h + vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) + vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h ++vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h + vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h + vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) + vcfroh.o: vcfroh.c $(roh_h) +@@ -157,22 +150,22 @@ + vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) + vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) + vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) +-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) ++reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(bcftools_h) + tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) +-ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h) ++ccall.o: ccall.c $(call_h) kmin.h $(prob1_h) + convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) + tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) + em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) +-filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) ++filter.o: filter.c $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) + gvcf.o: gvcf.c $(call_h) + kmin.o: kmin.c kmin.h +-mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h) ++mcall.o: mcall.c $(call_h) + prob1.o: prob1.c $(prob1_h) + vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h +-ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h) ++ploidy.o: ploidy.c $(htslib_regidx_h) $(htslib_hts_h) $(bcftools_h) $(ploidy_h) + polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h +-peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h +-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h ++peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) ++consensus.o: consensus.c $(htslib_hts_h) rbuf.h $(bcftools_h) + version.o: version.h version.c -@@ -158,8 +156,8 @@ + test/test-rbuf.o: test/test-rbuf.c rbuf.h +@@ -180,8 +173,8 @@ test/test-rbuf: test/test-rbuf.o - $(CC) $(CFLAGS) -o $@ -lm -ldl $< + $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) -bcftools: $(HTSLIB) $(OBJS) -- $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS) +- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) +bcftools: $(OBJS) -+ $(CC) $(CFLAGS) -o $@ $(OBJS) -lpthread -lz -lm -ldl -lhts $(LDLIBS) ++ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) -lhts -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) doc/bcftools.1: doc/bcftools.txt cd doc && a2x -adate="$(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 |