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jlec 14/09/25 15:20:53 |
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Added: samtools-1.0-buildsystem.patch |
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Log: |
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sci-biology/samtools: Install bam headers and create libbam.so, #523644 |
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(Portage version: 2.2.13/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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Revision Changes Path |
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1.1 sci-biology/samtools/files/samtools-1.0-buildsystem.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.0-buildsystem.patch?rev=1.1&view=markup |
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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 |
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|
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Index: samtools-1.0-buildsystem.patch |
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=================================================================== |
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Makefile | 26 ++++++++++++++++++-------- |
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1 file changed, 18 insertions(+), 8 deletions(-) |
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diff --git a/Makefile b/Makefile |
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index ae59abf..0d2788c 100644 |
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--- a/Makefile |
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+++ b/Makefile |
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@@ -21,11 +21,12 @@ |
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
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# DEALINGS IN THE SOFTWARE. |
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|
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-CC = gcc |
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-CPPFLAGS = $(DFLAGS) $(INCLUDES) |
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-CFLAGS = -g -Wall -O2 |
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-LDFLAGS = |
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-LDLIBS = |
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+CC ?= gcc |
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+CPPFLAGS += $(DFLAGS) $(INCLUDES) |
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+CFLAGS ?= -g -Wall -O2 |
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+LDFLAGS += |
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+LDLIBS += |
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+BAMLIB ?= libbam.a |
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DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 |
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LOBJS= bam_aux.o bam.o bam_import.o sam.o \ |
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sam_header.o bam_plbuf.o |
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@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses |
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prefix = /usr/local |
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exec_prefix = $(prefix) |
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bindir = $(exec_prefix)/bin |
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+bindir = $(exec_prefix)/lib |
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mandir = $(prefix)/share/man |
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man1dir = $(mandir)/man1 |
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|
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@@ -115,14 +117,22 @@ version.h: |
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.c.o: |
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$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
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|
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+$(LOBJS): |
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+ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< |
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-lib:libbam.a |
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+ |
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+lib:libbam.a libbam.so.1.0 |
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|
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libbam.a:$(LOBJS) |
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$(AR) -csru $@ $(LOBJS) |
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-samtools: $(AOBJS) libbam.a $(HTSLIB) |
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- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
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+libbam.so.1.0:$(LOBJS) |
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+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz |
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+ ln -sf $@ libbam.so.0 |
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+ ln -sf $@ libbam.so |
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+ |
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+samtools: $(AOBJS) $(HTSLIB) lib |
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+ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz |
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bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) |
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bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h |
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