diff options
Diffstat (limited to 'sci-biology/samtools/files/samtools-1.2-buildsystem.patch')
| -rw-r--r-- | sci-biology/samtools/files/samtools-1.2-buildsystem.patch | 193 |
1 files changed, 0 insertions, 193 deletions
diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch deleted file mode 100644 index 2343b2245a29..000000000000 --- a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch +++ /dev/null @@ -1,193 +0,0 @@ - Makefile | 94 +++++++++++++++++++++++++++++++++++----------------------------- - 1 file changed, 52 insertions(+), 42 deletions(-) - -diff --git a/Makefile b/Makefile -index e368cee..9054526 100644 ---- a/Makefile -+++ b/Makefile -@@ -21,11 +21,12 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --CPPFLAGS = $(DFLAGS) $(INCLUDES) --CFLAGS = -g -Wall -O2 --LDFLAGS = --LDLIBS = -+CC ?= gcc -+CPPFLAGS += $(DFLAGS) $(INCLUDES) -+CFLAGS ?= -g -Wall -O2 -+LDFLAGS += -+LDLIBS += -+BAMLIB ?= libbam.a - 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 -@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses - prefix = /usr/local - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin -+libdir = $(exec_prefix)/lib - mandir = $(prefix)/share/man - man1dir = $(mandir)/man1 - -@@ -115,62 +117,70 @@ version.h: - .c.o: - $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< - -+$(LOBJS): -+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< - --lib:libbam.a -+ -+lib:libbam.a libbam.so.1.0 - - libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - --samtools: $(AOBJS) libbam.a $(HTSLIB) -- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz -+libbam.so.1.0:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz -+ ln -sf $@ libbam.so.0 -+ ln -sf $@ libbam.so -+ -+samtools: $(AOBJS) lib -+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz - - bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) - bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h - bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) - bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) --bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) -+bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) - sam_h = sam.h $(htslib_sam_h) $(bam_h) --sample_h = sample.h $(HTSDIR)/htslib/kstring.h -+sample_h = sample.h - - bam.o: bam.c $(bam_h) sam_header.h --bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h -+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h - bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h - bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h - bam_aux.o: bam_aux.c - bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) - bam_color.o: bam_color.c $(bam_h) --bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h --bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h --bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h -+bam_import.o: bam_import.c $(bam_h) -+bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) -+bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) - bam_mate.o: bam_mate.c $(bam_h) - bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h - bam_pileup.o: bam_pileup.c $(sam_h) - bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) --bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) -+bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) - bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) --bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h --bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h --bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) -+bam_rmdup.o: bam_rmdup.c $(sam_h) -+bam_rmdupse.o: bam_rmdupse.c $(sam_h) -+bam_sort.o: bam_sort.c $(htslib_sam_h) - bam_stat.o: bam_stat.c $(bam_h) samtools.h - bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) - bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) - bam_tview_html.o: bam_tview_html.c $(bam_tview_h) - bam_flags.o: bam_flags.c $(sam_h) --bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h -+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h - bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h --bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h --bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h -+bedcov.o: bedcov.c $(htslib_sam_h) -+bedidx.o: bedidx.c - cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) --errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h -+errmod.o: errmod.c errmod.h - kprobaln.o: kprobaln.c kprobaln.h - padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) --phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h -+phase.o: phase.c $(htslib_sam_h) errmod.h - sam.o: sam.c $(htslib_faidx_h) $(sam_h) --sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h --sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h --sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h --stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h --stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) -+sam_header.o: sam_header.c sam_header.h -+sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h -+sample.o: sample.c $(sample_h) -+stats_isize.o: stats_isize.c stats_isize.h -+stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) - - - # test programs -@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib - # 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) $(BUILT_TEST_PROGRAMS) -- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) -+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 - test/merge/test_rtrans_build -@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - test/split/test_parse_args - - --test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) -+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 $(HTSLIB) $(LDLIBS) -lz - --test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) -+test/merge/test_pretty_header: test/merge/test_pretty_header.o - $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz - --test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) -+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o - $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz - --test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) -+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o - $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz - --test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) -+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 $(HTSLIB) $(LDLIBS) -lz - --test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) -+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 $(HTSLIB) $(LDLIBS) -lz - --test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) -+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 $(HTSLIB) $(LDLIBS) -lz - --test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) -+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 $(HTSLIB) $(LDLIBS) -lz - --test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) -+test/vcf-miniview: test/vcf-miniview.o - $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz - - test_test_h = test/test.h $(htslib_sam_h) -@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o - misc/wgsim: misc/wgsim.o - $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz - --misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h -+misc/ace2sam.o: misc/ace2sam.c - misc/md5.o: misc/md5.c misc/md5.h --misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h --misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h -+misc/md5fa.o: misc/md5fa.c misc/md5.h -+misc/wgsim.o: misc/wgsim.c - - misc/maq2sam-short.o: misc/maq2sam.c - $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c |