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path: root/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
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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.patch183
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