[med-svn] [dwgsim] 02/05: Fix debianising of makefile

[Kevin Murray]

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

commit a9c5a6521286b3a86e11910d3c582de1f9f3ebda
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Mon Oct 26 11:46:54 2015 +1100

    Fix debianising of makefile
---
 debian/patches/0001-Debian-ise-makefile.patch | 49 +++++++++++++++++----------
 1 file changed, 31 insertions(+), 18 deletions(-)

diff --git a/debian/patches/0001-Debian-ise-makefile.patch b/debian/patches/0001-Debian-ise-makefile.patch
index 9b9a3dc..578a815 100644
--- a/debian/patches/0001-Debian-ise-makefile.patch
+++ b/debian/patches/0001-Debian-ise-makefile.patch
@@ -2,19 +2,20 @@ From: Kevin Murray <spam at kdmurray.id.au>
 Date: Wed, 23 Sep 2015 10:15:35 +1000
 Subject: Debian-ise makefile
 
+
+Fix parts of the makefile patching
 ---
- Makefile | 65 +++++++++-------------------------------------------------------
- 1 file changed, 9 insertions(+), 56 deletions(-)
+ Makefile | 82 ++++++++++++++++------------------------------------------------
+ 1 file changed, 20 insertions(+), 62 deletions(-)
 
 diff --git a/Makefile b/Makefile
-index 0d5b9ec..3972f0f 100644
+index 0d5b9ec..f65e6ea 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -1,73 +1,26 @@
+@@ -1,73 +1,31 @@
 -PACKAGE_VERSION="0.1.11"
-+PACKAGE_VERSION=$(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ')
- CC=			gcc
- CFLAGS=		-g -Wall -O3 #-m64 #-arch ppc
+-CC=			gcc
+-CFLAGS=		-g -Wall -O3 #-m64 #-arch ppc
 -DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\\\"${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
@@ -23,22 +24,34 @@ index 0d5b9ec..3972f0f 100644
 -					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=\"${PACKAGE_VERSION}\"
-+DWGSIM_AOBJS =	src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o \
-+		src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o
- 
+-
 -PROG=		dwgsim dwgsim_eval
-+PROG=		dwgsim
- INCLUDES=	-I.
+-INCLUDES=	-I.
 -SUBDIRS=	samtools . 
 -CLEAN_SUBDIRS=	samtools src
 -LIBPATH=
++PACKAGE_VERSION=$(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ')
++CC       ?=	gcc
++CFLAGS   +=	-Wall -O3 -I.
++CPPFLAGS +=	-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"
++PROG      =	dwgsim
++
++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
  
  .SUFFIXES:.c .o
++.PHONY:all clean cleanlocal
  
  .c.o:
- 		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
- 
+-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+-
 -all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 -		@target=`echo $@ | sed s/-recur//`; \
 -		wdir=`pwd`; \
@@ -48,13 +61,13 @@ index 0d5b9ec..3972f0f 100644
 -				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
 -			cd $$wdir; \
 -		done;
--
++	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+ 
  all:$(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

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