diff options
Diffstat (limited to 'sci-biology/samtools/files/samtools-1.3-buildsystem.patch')
| -rw-r--r-- | sci-biology/samtools/files/samtools-1.3-buildsystem.patch | 174 |
1 files changed, 174 insertions, 0 deletions
diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch new file mode 100644 index 000000000000..61f6b03bd8ef --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch @@ -0,0 +1,174 @@ +--- samtools-1.3/Makefile ++++ samtools-1.3/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 = +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LIBS = ++CC ?= gcc ++CPPFLAGS += ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LIBS += ++BAMLIB ?= libbam.a + + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ +@@ -42,6 +43,7 @@ + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++libdir ?= $(exec_prefix)/lib + datarootdir = $(prefix)/share + mandir = $(datarootdir)/man + man1dir = $(mandir)/man1 +@@ -129,67 +131,74 @@ + .c.o: + $(CC) $(CFLAGS) $(ALL_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 $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.1 ++ 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) $(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) + sam_opts_h = sam_opts.h $(htslib_hts_h) +-sample_h = sample.h $(htslib_kstring_h) ++sample_h = sample.h + + bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h +-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(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 $(htslib_khash_h) $(htslib_ksort_h) + bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) + bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) + bam_aux.o: bam_aux.c $(bam_h) + bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) + bam_color.o: bam_color.c $(bam_h) +-bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(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 $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) + bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_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) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_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_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) + bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +-bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) +-bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) +-bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_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_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) + bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h + bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) + bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c $(bam_tview_h) + bam_flags.o: bam_flags.c $(htslib_sam_h) +-bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) ++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h + bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h +-bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +-bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) ++bedcov.o: bedcov.c $(htslib_sam_h) ++bedidx.o: bedidx.c + cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) + dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) +-errmod.o: errmod.c errmod.h $(htslib_ksort_h) ++errmod.o: errmod.c errmod.h + kprobaln.o: kprobaln.c kprobaln.h + padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) +-phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(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 $(htslib_khash_h) ++sam_header.o: sam_header.c sam_header.h + sam_opts.o: sam_opts.c $(sam_opts_h) +-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +-sample.o: sample.c $(sample_h) $(htslib_khash_h) +-stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) +-stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_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 +@@ -197,8 +206,8 @@ + # 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_rtrans_build + test/merge/test_trans_tbl_init +@@ -210,28 +219,28 @@ + test/split/test_parse_args + + +-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) ++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) ++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) ++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_count_rg: test/split/test_count_rg.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_parse_args: test/split/test_parse_args.o test/test.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) ++test/vcf-miniview: test/vcf-miniview.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) + + test_test_h = test/test.h $(htslib_sam_h) |