diff options
| -rw-r--r-- | .SRCINFO | 2 | ||||
| -rw-r--r-- | PKGBUILD | 8 | ||||
| -rw-r--r-- | makefile-system-htslib.patch | 99 |
3 files changed, 13 insertions, 96 deletions
@@ -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 @@ -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 864ac22bc7a6..bd46ac328d44 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 |