diff options
author | Christian Krause | 2015-06-13 11:56:57 +0200 |
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committer | Christian Krause | 2015-06-13 11:56:57 +0200 |
commit | c80418d7478821cd4e286784fd9d5667e0240b3d (patch) | |
tree | a660287793f686f169267a31dcffa081df08b8e5 /makefile-system-htslib.patch | |
download | aur-c80418d7478821cd4e286784fd9d5667e0240b3d.tar.gz |
Initial import
Diffstat (limited to 'makefile-system-htslib.patch')
-rw-r--r-- | makefile-system-htslib.patch | 96 |
1 files changed, 96 insertions, 0 deletions
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch new file mode 100644 index 000000000000..864ac22bc7a6 --- /dev/null +++ b/makefile-system-htslib.patch @@ -0,0 +1,96 @@ +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 @@ + + + # 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) + |