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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, 0 insertions, 183 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
deleted file mode 100644
index d5ff3bd45da5..000000000000
--- a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
+++ /dev/null
@@ -1,183 +0,0 @@
- 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