jlec 14/09/25 15:20:53 Added: samtools-1.0-buildsystem.patch Log: sci-biology/samtools: Install bam headers and create libbam.so, #523644 (Portage version: 2.2.13/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path 1.1 sci-biology/samtools/files/samtools-1.0-buildsystem.patch file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.0-buildsystem.patch?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.0-buildsystem.patch?rev=1.1&content-type=text/plain Index: samtools-1.0-buildsystem.patch =================================================================== Makefile | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/Makefile b/Makefile index ae59abf..0d2788c 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 +bindir = $(exec_prefix)/lib mandir = $(prefix)/share/man man1dir = $(mandir)/man1 @@ -115,14 +117,22 @@ 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) $(HTSLIB) 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
