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authorChristian Krause2017-03-14 07:32:58 +0100
committerChristian Krause2017-03-14 07:32:58 +0100
commit292712615848a243ff84e54e972cb14252c13fb0 (patch)
treeebb81913552cbadc834d72d909eea71f71f1c3d6
parent6909f32c308a8ac079f7bc711fe1ca45c0a9371b (diff)
downloadaur-292712615848a243ff84e54e972cb14252c13fb0.tar.gz
bcftools-1.4-1
-rw-r--r--.SRCINFO10
-rw-r--r--PKGBUILD13
-rw-r--r--makefile-system-htslib.patch60
3 files changed, 50 insertions, 33 deletions
diff --git a/.SRCINFO b/.SRCINFO
index ab1d2cdd9a8..99892a6c7dd 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,8 +1,8 @@
# Generated by mksrcinfo v8
-# Sun May 29 18:21:54 UTC 2016
+# Tue Mar 14 06:32:07 UTC 2017
pkgbase = bcftools
pkgdesc = Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
- pkgver = 1.3.1
+ pkgver = 1.4
pkgrel = 1
url = http://samtools.github.io/bcftools/
arch = i686
@@ -10,10 +10,10 @@ pkgbase = bcftools
license = GPL
depends = gsl
depends = htslib
- source = https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
+ source = https://github.com/samtools/bcftools/releases/download/1.4/bcftools-1.4.tar.bz2
source = makefile-system-htslib.patch
- md5sums = 575001e9fca37cab0c7a7287ad4b1cdb
- md5sums = 3547e133251f4d088cb087019183efa7
+ md5sums = 50ccf0a073bd70e99cdb3c8be830416e
+ md5sums = baba7d2fc8947c7ec29ff4498637ea85
pkgname = bcftools
diff --git a/PKGBUILD b/PKGBUILD
index f879c2dc869..27488461465 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,23 +1,21 @@
-# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+# Maintainer: Christian Krause ("wookietreiber") <christian.krause@mailbox.org>
pkgname=bcftools
-pkgver=1.3.1
+pkgver=1.4
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')
-source=(https://github.com/samtools/$pkgname/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2
+source=(https://github.com/samtools/bcftools/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2
makefile-system-htslib.patch)
-md5sums=('575001e9fca37cab0c7a7287ad4b1cdb'
- '3547e133251f4d088cb087019183efa7')
prepare() {
cd $srcdir/$pkgname-$pkgver
# prevent shipped htslib to be used
- rm -rf htslib-1.3.1
+ rm -rf htslib-$pkgver
# patch Makefile to make it work with a system-provided htslib
patch -i $srcdir/makefile-system-htslib.patch
@@ -40,3 +38,6 @@ package() {
make prefix=/usr plugindir=/usr/lib/$pkgname USE_GPL=1 DESTDIR=$pkgdir install
}
+
+md5sums=('50ccf0a073bd70e99cdb3c8be830416e'
+ 'baba7d2fc8947c7ec29ff4498637ea85')
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch
index 7ae2b4c6f29..5cebf3c5d3b 100644
--- a/makefile-system-htslib.patch
+++ b/makefile-system-htslib.patch
@@ -1,16 +1,17 @@
-diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched/Makefile
---- /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile 2016-04-22 11:50:59.000000000 +0200
-+++ /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched/Makefile 2016-05-29 20:18:22.323268586 +0200
-@@ -28,18 +28,10 @@
-
+--- 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-1.3.1
+ # Adjust $(HTSDIR) to point to your top-level htslib directory
+-HTSDIR = htslib-1.4
-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
@@ -20,10 +21,21 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool
-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 $(LIBS)
+
OBJS = main.o vcfindex.o tabix.o \
- vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
-@@ -48,7 +40,7 @@
- vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
+@@ -64,7 +54,7 @@
+ mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
@@ -31,7 +43,7 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool
GSL_LIBS =
# The polysomy command is not compiled by default because it brings dependency
-@@ -57,7 +49,7 @@
+@@ -73,7 +63,7 @@
ifdef USE_GPL
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
@@ -40,13 +52,14 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool
endif
prefix = /usr/local
-@@ -101,11 +93,11 @@
+@@ -117,12 +107,12 @@
.c.o:
- $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
+ $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
--test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
+-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: $(PROG) plugins test/test-rbuf
+ ./test/test.pl --exec bgzip=bgzip --exec tabix=tabix
-test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
@@ -56,16 +69,19 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool
# Plugin rules
-@@ -180,8 +172,8 @@
- test/test-rbuf: test/test-rbuf.o
- $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
+@@ -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) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+- $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
+bcftools: $(OBJS)
-+ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) -lhts -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
++ $(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
-Only in /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched: Makefile.orig
-Only in /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched: Makefile.rej