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authorChristian Krause2015-06-30 16:06:16 +0200
committerChristian Krause2015-06-30 16:06:16 +0200
commit44f20a96a7bfb6d31869227405398bf4ac721b24 (patch)
tree5952bb30c8f697b4169099f2bf3bda0636510b23
parent2bcd42cf6974d60c05fc5abfc524295a05f17259 (diff)
downloadaur-44f20a96a7bfb6d31869227405398bf4ac721b24.tar.gz
simplified Makefile patch
-rw-r--r--.SRCINFO2
-rw-r--r--PKGBUILD8
-rw-r--r--makefile-system-htslib.patch99
3 files changed, 13 insertions, 96 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 497a5cc2d9c..0bcdf395acc 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -14,7 +14,7 @@ pkgbase = samtools
source = samtools-1.2.tar.gz::https://github.com/samtools/samtools/archive/1.2.tar.gz
source = makefile-system-htslib.patch
md5sums = 2748356ef392c0694ca1142de37cf2aa
- md5sums = 05b136769fff4ab6c0962877390e96d8
+ md5sums = 00f3b0b730f37cd7c8ff12376a9a0c6a
pkgname = samtools
diff --git a/PKGBUILD b/PKGBUILD
index 017105d7c63..e7fbf500207 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -15,7 +15,7 @@ options=('staticlibs')
source=($pkgname-$pkgver.tar.gz::https://github.com/samtools/samtools/archive/$pkgver.tar.gz
makefile-system-htslib.patch)
md5sums=('2748356ef392c0694ca1142de37cf2aa'
- '05b136769fff4ab6c0962877390e96d8')
+ '00f3b0b730f37cd7c8ff12376a9a0c6a')
prepare() {
cd $srcdir/$pkgname-$pkgver
@@ -30,19 +30,19 @@ prepare() {
build() {
cd $srcdir/$pkgname-$pkgver
- make
+ make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts
}
check() {
cd $srcdir/$pkgname-$pkgver
- make check
+ make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts check
}
package() {
cd $srcdir/$pkgname-$pkgver
- make DESTDIR=$pkgdir prefix=/usr install
+ make HTSDIR=/usr/include HTSLIB= BGZIP= LDLIBS=-lhts DESTDIR=$pkgdir prefix=/usr install
for file in misc/*.lua ; do
install -Dm755 $file $pkgdir/usr/bin/$(basename $file)
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch
index 864ac22bc7a..bd46ac328d4 100644
--- a/makefile-system-htslib.patch
+++ b/makefile-system-htslib.patch
@@ -1,96 +1,13 @@
diff -aur samtools-1.2/Makefile samtools-1.2-patched/Makefile
--- samtools-1.2/Makefile 2015-02-02 16:18:41.000000000 +0100
-+++ samtools-1.2-patched/Makefile 2015-02-04 11:58:14.059908160 +0100
-@@ -25,7 +25,7 @@
- CPPFLAGS = $(DFLAGS) $(INCLUDES)
- CFLAGS = -g -Wall -O2
- LDFLAGS =
--LDLIBS =
-+LDLIBS = -lhts
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \
- sam_header.o bam_plbuf.o
-@@ -82,10 +82,8 @@
-
++++ samtools-1.2-patched/Makefile 2015-06-30 15:48:41.006563956 +0200
+@@ -83,7 +83,9 @@
# Adjust $(HTSDIR) to point to your top-level htslib directory
--HTSDIR = ../htslib
--include $(HTSDIR)/htslib.mk
--HTSLIB = $(HTSDIR)/libhts.a
--BGZIP = $(HTSDIR)/bgzip
-+HTSDIR = /usr/include
-+BGZIP = bgzip
-
-
- PACKAGE_VERSION = 1.2
-@@ -121,8 +119,8 @@
- libbam.a:$(LOBJS)
- $(AR) -csru $@ $(LOBJS)
-
--samtools: $(AOBJS) libbam.a $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
-+samtools: $(AOBJS) libbam.a
-+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(LDLIBS) $(LIBCURSES) -lm -lz
-
- bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
- bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
-@@ -178,7 +176,7 @@
- # For tests that might use it, set $REF_PATH explicitly to use only reference
- # areas within the test suite (or set it to ':' to use no reference areas).
- # (regression.sh sets $REF_PATH to a subdirectory itself.)
--check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
-+check test: samtools $(BUILT_TEST_PROGRAMS)
- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
- test/merge/test_bam_translate test/merge/test_bam_translate.tmp
- test/merge/test_pretty_header
-@@ -191,32 +189,32 @@
- test/split/test_parse_args
-
-
--test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(LDLIBS) -lz
-
--test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_pretty_header: test/merge/test_pretty_header.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(LDLIBS) -lz
-
--test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(LDLIBS) -lz
-
--test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz
-+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(LDLIBS) -lz
-
--test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_count_rg: test/split/test_count_rg.o test/test.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(LDLIBS) -lz
-
--test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(LDLIBS) -lz
-
--test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(LDLIBS) -lz
-
--test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-+test/split/test_parse_args: test/split/test_parse_args.o test/test.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(LDLIBS) -lz
-
--test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
-- $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz
-+test/vcf-miniview: test/vcf-miniview.o
-+ $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(LDLIBS) -lz
-
- test_test_h = test/test.h $(htslib_sam_h)
+ HTSDIR = ../htslib
++ifneq ("$(wildcard $(HTSDIR)/htslib.mk)","")
+ include $(HTSDIR)/htslib.mk
++endif
+ HTSLIB = $(HTSDIR)/libhts.a
+ BGZIP = $(HTSDIR)/bgzip