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| author |   Ted Tanberry <ted.tanberry@gmail.com> | 2015-02-05 20:20:03 +0100 |
|---|---|---|
| committer | Ted Tanberry <ted.tanberry@gmail.com> | 2015-02-05 20:20:03 +0100 |
| commit | b4649db619f8514efb9377422de3ea42154b3a80 (patch) | |
| tree | 21fcb4fc0fb477238c4ce29f6336c1fd8605f595 /sci-biology/bwa/files | |
| parent | Fixed emboss-r1.eclass to depend on virtual/mysql and not dev-db/mysql. (diff) | |
| download | sci-b4649db619f8514efb9377422de3ea42154b3a80.tar.gz sci-b4649db619f8514efb9377422de3ea42154b3a80.tar.bz2 sci-b4649db619f8514efb9377422de3ea42154b3a80.zip | |
Updated bwa to 0.7.12 and modernized the build system. Removed hard-coded ar.
Diffstat (limited to 'sci-biology/bwa/files')
| -rw-r--r-- | sci-biology/bwa/files/bwa_Makefile.patch | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/sci-biology/bwa/files/bwa_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch new file mode 100644 index 000000000..406e9b052 --- /dev/null +++ b/sci-biology/bwa/files/bwa_Makefile.patch @@ -0,0 +1,27 @@ +--- Makefile ++++ Makefile +@@ -1,8 +1,8 @@ +-CC= gcc ++CC?= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS?= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar ++AR?= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o + AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -26,10 +26,10 @@ + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) |