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authorChristian Krause2016-03-05 11:40:11 +0100
committerChristian Krause2016-03-05 11:40:11 +0100
commit295038a40f0e6bafafc7765250919f555557a74a (patch)
treeb66c12a93ecfe2c68e1a7a422d6b1f5231ddf762
parentce0e65b4a554c65329bc40d6de30120fda1aa0ea (diff)
downloadaur-295038a40f0e6bafafc7765250919f555557a74a.tar.gz
bcftools-1.3-2
-rw-r--r--.SRCINFO7
-rw-r--r--PKGBUILD12
-rw-r--r--makefile-system-htslib.patch28
3 files changed, 26 insertions, 21 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 8ec76a8b525..3ddf4e27987 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,20 +1,19 @@
# Generated by mksrcinfo v8
-# Sun Jan 10 10:43:34 UTC 2016
+# Sat Mar 5 10:39:13 UTC 2016
pkgbase = bcftools
pkgdesc = Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
pkgver = 1.3
- pkgrel = 1
+ pkgrel = 2
url = http://samtools.github.io/bcftools/
arch = i686
arch = x86_64
license = GPL
- depends = gsl
depends = htslib
depends = perl
source = https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2
source = makefile-system-htslib.patch
md5sums = 17f1f7d9e4a03d64a114b43ca896899f
- md5sums = 697d169f4a729c0fc61720490b60ea5e
+ md5sums = e5145d175dcd242634baf42749b838f0
pkgname = bcftools
diff --git a/PKGBUILD b/PKGBUILD
index 9f21ce0cc10..24fec0d000e 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,16 +2,16 @@
pkgname=bcftools
pkgver=1.3
-pkgrel=1
+pkgrel=2
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')
+depends=('htslib' 'perl') # 'gsl'
source=(https://github.com/samtools/$pkgname/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2
makefile-system-htslib.patch)
md5sums=('17f1f7d9e4a03d64a114b43ca896899f'
- '697d169f4a729c0fc61720490b60ea5e')
+ 'e5145d175dcd242634baf42749b838f0')
prepare() {
cd $srcdir/$pkgname-$pkgver
@@ -26,17 +26,17 @@ prepare() {
build() {
cd $srcdir/$pkgname-$pkgver
- make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1
+ make prefix=/usr plugindir=/usr/lib/$pkgname # USE_GPL=1
}
check() {
cd $srcdir/$pkgname-$pkgver
- make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 test
+ make prefix=/usr plugindir=/usr/lib/$pkgname # USE_GPL=1 test
}
package() {
cd $srcdir/$pkgname-$pkgver
- make -e prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 DESTDIR=$pkgdir install
+ make prefix=/usr plugindir=/usr/lib/$pkgname DESTDIR=$pkgdir install # USE_GPL=1
}
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch
index 9965be1135d..91056165a42 100644
--- a/makefile-system-htslib.patch
+++ b/makefile-system-htslib.patch
@@ -1,6 +1,6 @@
---- Makefile.orig 2016-01-10 11:15:35.126733492 +0100
-+++ Makefile 2016-01-10 11:21:31.034859116 +0100
-@@ -28,13 +28,6 @@
+--- /tmp/bcftools-1.3/Makefile 2015-12-15 22:58:35.000000000 +0100
++++ /tmp/makepkg/bcftools/src/bcftools-1.3/Makefile 2016-03-05 11:24:58.512091814 +0100
+@@ -28,18 +28,8 @@
all: $(PROG) $(TEST_PROG)
@@ -12,9 +12,15 @@
-TABIX = $(HTSDIR)/tabix
-
CC = gcc
- CPPFLAGS =
- CFLAGS = -g -Wall -Wc++-compat -O2
-@@ -48,7 +41,7 @@
+-CPPFLAGS =
+-CFLAGS = -g -Wall -Wc++-compat -O2
+-LDFLAGS =
+-LIBS =
++CFLAGS := -g -Wall -Wc++-compat -O2 $(CFLAGS)
+
+ OBJS = main.o vcfindex.o tabix.o \
+ vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
+@@ -48,7 +38,7 @@
vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
@@ -23,7 +29,7 @@
GSL_LIBS =
# The polysomy command is not compiled by default because it brings dependency
-@@ -57,7 +50,7 @@
+@@ -57,7 +47,7 @@
ifdef USE_GPL
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
@@ -32,7 +38,7 @@
endif
prefix = /usr/local
-@@ -101,11 +94,11 @@
+@@ -101,11 +91,11 @@
.c.o:
$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
@@ -48,7 +54,7 @@
# Plugin rules
-@@ -136,20 +129,20 @@
+@@ -136,20 +126,20 @@
filter_h = filter.h $(htslib_vcf_h)
ploidy_h = ploidy.h $(htslib_regidx_h)
prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
@@ -75,7 +81,7 @@
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 @@
+@@ -157,22 +147,22 @@
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)
@@ -105,7 +111,7 @@
version.o: version.h version.c
test/test-rbuf.o: test/test-rbuf.c rbuf.h
-@@ -180,8 +173,8 @@
+@@ -180,8 +170,8 @@
test/test-rbuf: test/test-rbuf.o
$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)