[med-svn] [dwgsim] 03/03: Patch makefile

[Kevin Murray]

This is an automated email from the git hooks/post-receive script.

daube-guest pushed a commit to branch master
in repository dwgsim.

commit 49ce9326d62b6f5c5a1f3477756e24fc9915a029
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Wed Sep 23 10:16:12 2015 +1000

    Patch makefile
---
 debian/patches/0001-Debian-ise-makefile.patch | 95 +++++++++++++++++++++++++++
 debian/patches/series                         |  1 +
 2 files changed, 96 insertions(+)

diff --git a/debian/patches/0001-Debian-ise-makefile.patch b/debian/patches/0001-Debian-ise-makefile.patch
new file mode 100644
index 0000000..9b9a3dc
--- /dev/null
+++ b/debian/patches/0001-Debian-ise-makefile.patch
@@ -0,0 +1,95 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Wed, 23 Sep 2015 10:15:35 +1000
+Subject: Debian-ise makefile
+
+---
+ Makefile | 65 +++++++++-------------------------------------------------------
+ 1 file changed, 9 insertions(+), 56 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 0d5b9ec..3972f0f 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,73 +1,26 @@
+-PACKAGE_VERSION="0.1.11"
++PACKAGE_VERSION=$(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ')
+ CC=			gcc
+ CFLAGS=		-g -Wall -O3 #-m64 #-arch ppc
+-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\\\"${PACKAGE_VERSION}\\\"
+-DWGSIM_AOBJS = src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o \
+-			   src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o
+-DWGSIM_EVAL_AOBJS = src/dwgsim_eval.o \
+-					samtools/knetfile.o \
+-					samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o \
+-					samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/bedidx.o \
+-					samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/bam_cat.o
++DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"
++DWGSIM_AOBJS =	src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o \
++		src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o
+ 
+-PROG=		dwgsim dwgsim_eval
++PROG=		dwgsim
+ INCLUDES=	-I.
+-SUBDIRS=	samtools . 
+-CLEAN_SUBDIRS=	samtools src
+-LIBPATH=
+ 
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+ 		$(CC) -c $(CFLAGS) $(DFLAGS) $(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)" \
+-				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+-			cd $$wdir; \
+-		done;
+-
+ all:$(PROG)
+ 
+-.PHONY:all lib clean cleanlocal
+-.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
++.PHONY:all clean cleanlocal
+ 
+-dwgsim:lib-recur $(DWGSIM_AOBJS)
++dwgsim: $(DWGSIM_AOBJS)
+ 	$(CC) $(CFLAGS) -o $@ $(DWGSIM_AOBJS) -lm -lz -lpthread
+ 
+-dwgsim_eval:lib-recur $(DWGSIM_EVAL_AOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(DWGSIM_EVAL_AOBJS) -Lsamtools -lm -lz -lpthread
+-
+ cleanlocal:
+-		rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib; \
+-		wdir=`pwd`; \
+-		list='$(CLEAN_SUBDIRS)'; for subdir in $$list; do \
+-			if [ -d $$subdir ]; then \
+-				cd $$subdir; \
+-				pwd; \
+-				rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib; \
+-				cd $$wdir; \
+-			fi; \
+-		done;
+-
+-clean:cleanlocal-recur
++	rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib;
+ 
+-dist:clean
+-	if [ -f dwgsim-${PACKAGE_VERSION}.tar.gz ]; then \
+-        rm -rv dwgsim-${PACKAGE_VERSION}.tar.gz; \
+-	fi; \
+-	if [ -f dwgsim-${PACKAGE_VERSION}.tar ]; then \
+-        rm -rv dwgsim-${PACKAGE_VERSION}.tar; \
+-	fi; \
+-	if [ -d dwgsim-${PACKAGE_VERSION} ]; then \
+-        rm -rv dwgsim-${PACKAGE_VERSION}; \
+-	fi; \
+-    mkdir dwgsim-${PACKAGE_VERSION}; \
+-	cp -r INSTALL LICENSE Makefile README scripts src dwgsim-${PACKAGE_VERSION}/.; \
+-	tar -vcf dwgsim-${PACKAGE_VERSION}.tar dwgsim-${PACKAGE_VERSION}; \
+-	gzip -9 dwgsim-${PACKAGE_VERSION}.tar; \
+-	rm -rv dwgsim-${PACKAGE_VERSION};
++clean:cleanlocal
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..09a670c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+0001-Debian-ise-makefile.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/dwgsim.git