diff options
Diffstat (limited to 'sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch')
-rw-r--r-- | sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch | 183 |
1 files changed, 183 insertions, 0 deletions
diff --git a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch new file mode 100644 index 000000000000..d5ff3bd45da5 --- /dev/null +++ b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch @@ -0,0 +1,183 @@ + Makefile | 22 +++++++++++----------- + bcftools/Makefile | 12 ++++++------ + misc/Makefile | 28 ++++++++++++++-------------- + 3 files changed, 31 insertions(+), 31 deletions(-) + +diff --git a/Makefile b/Makefile +index 2f51bfc..4dda5a4 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 +-#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 ++CC?= gcc ++CFLAGS?= -g -Wall -O2 ++#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ + bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ +@@ -21,14 +21,14 @@ LIBCURSES= -lcurses # -lXCurses + .PHONY: all lib + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all-recur lib-recur clean-recur cleanlocal-recur install-recur: + @target=`echo $@ | sed s/-recur//`; \ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -44,16 +44,16 @@ libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + + samtools:lib-recur $(AOBJS) +- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread + + bgzf.o:bgzf.c bgzf.h +- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS) + libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -lm -lpthread + + dylib: + @$(MAKE) cleanlocal; \ +diff --git a/bcftools/Makefile b/bcftools/Makefile +index be831de..7ef796c 100644 +--- a/bcftools/Makefile ++++ b/bcftools/Makefile +@@ -1,6 +1,6 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE ++CC?= gcc ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o + OMISC= .. + AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o +@@ -11,14 +11,14 @@ SUBDIRS= . + .SUFFIXES:.c .o + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ + + all-recur lib-recur clean-recur cleanlocal-recur install-recur: + @target=`echo $@ | sed s/-recur//`; \ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + + bcftools:lib $(AOBJS) +- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread + + bcf.o:bcf.h + vcf.o:bcf.h +diff --git a/misc/Makefile b/misc/Makefile +index d36e7ac..7ae1dc3 100644 +--- a/misc/Makefile ++++ b/misc/Makefile +@@ -1,8 +1,8 @@ +-CC= gcc +-CXX= g++ +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc +-CXXFLAGS= $(CFLAGS) +-DFLAGS= -D_FILE_OFFSET_BITS=64 ++CC?= gcc ++CXX?= g++ ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CXXFLAGS?= $(CFLAGS) ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 + OBJS= + PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck + INCLUDES= -I.. +@@ -11,7 +11,7 @@ SUBDIRS= . + .SUFFIXES:.c .o + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all:$(PROG) + +@@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: + lib: + + bamcheck:bamcheck.o +- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz + + bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h + $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c + + ace2sam:ace2sam.o +- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz + + md5sum-lite:md5sum-lite.o +- $(CC) $(CFLAGS) -o $@ md5sum-lite.o ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o + + md5sum-lite.o:md5.c md5.h + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz + + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c |