jlec 15/01/06 12:57:48 Added: samtools-1.1-buildsystem.patch Log: sci-biology/samtools: Version BUmp (Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path 1.1 sci-biology/samtools/files/samtools-1.1-buildsystem.patch file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.1-buildsystem.patch?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.1-buildsystem.patch?rev=1.1&content-type=text/plain Index: samtools-1.1-buildsystem.patch =================================================================== Makefile | 76 ++++++++++++++++++++++++++++++++++++---------------------------- 1 file changed, 43 insertions(+), 33 deletions(-) diff --git a/Makefile b/Makefile index 43cefc3..743dd07 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 @@ -115,63 +117,71 @@ 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 bam2bcf.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) kaln.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 $(bam_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 kaln.o: kaln.c kaln.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 @@ -179,8 +189,8 @@ 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 @@ -253,10 +263,10 @@ 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
