[med-svn] [scythe] 03/15: Add patches for 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 scythe.

commit c9ab57aa0cdb1471ecba50c062f09f8dcd6fab3c
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Mon Apr 27 16:09:10 2015 +1000

    Add patches for makefile
---
 .../0001-Makefile-cleaning-for-debian.patch        | 104 +++++++++++++++++++++
 debian/patches/series                              |   1 +
 2 files changed, 105 insertions(+)

diff --git a/debian/patches/0001-Makefile-cleaning-for-debian.patch b/debian/patches/0001-Makefile-cleaning-for-debian.patch
new file mode 100644
index 0000000..99da02d
--- /dev/null
+++ b/debian/patches/0001-Makefile-cleaning-for-debian.patch
@@ -0,0 +1,104 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Mon, 27 Apr 2015 16:04:30 +1000
+Subject: Makefile cleaning for debian
+
+---
+ Makefile | 53 +++++++++++++++++++++++++++++++++++------------------
+ 1 file changed, 35 insertions(+), 18 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index fec7050..3cabbbd 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,24 +1,31 @@
+ PROGRAM_NAME = scythe
+-VERSION = 0.991
++VERSION = 0.994
+ CC = gcc
+ DEBUG ?= 0
+-CFLAGS = -Wall -pedantic -DVERSION=$(VERSION) -std=gnu99
+ ifeq ($(DEBUG), 1)
+ 	CFLAGS += -g -O0
+-else 
++else
+ 	CFLAGS += -O3
+ endif
++
+ ARCHIVE = $(PROGRAM_NAME)_$(VERSION)
+-LDFLAGS = -lz -lm
++override CFLAGS += -Wall -pedantic -DVERSION=$(VERSION) -std=gnu99 -fPIC
++override LDFLAGS += -lz -lm
+ LDTESTFLAGS = -lcheck
+ SDIR = src
+-OBJS = match.o scythe.o util.o prob.o 
+-LOBJS = match.o util.o prob.o 
++LOBJS = match.o util.o prob.o
++OBJS = $(LOBJS) scythe.o
++
++.PHONY: clean distclean dist testclean lib test all debian debian-clean
+ 
++all: scythe test-scythe libscythe.so
+ 
+-.PHONY: clean default all distclean dist tests testclean lib
++# Executables
++scythe: $(OBJS)
++	$(CC) $(CFLAGS) $(OBJS) -o scythe $(LDFLAGS)
+ 
+-default: all
++test-scythe: $(LOBJS) tests.o
++	$(CC) $(CFLAGS) $(LOBJS) tests.o -o test-scythe $(LDFLAGS) $(LDTESTFLAGS)
+ 
+ %.o: $(SDIR)/%.c
+ 	$(CC) $(CFLAGS) -c $< -o $@
+@@ -27,31 +34,41 @@ match.o: $(SDIR)/scythe.h
+ scythe.o: $(SDIR)/kseq.h $(SDIR)/scythe.h
+ util.o: $(SDIR)/kseq.h $(SDIR)/scythe.h
+ prob.o: $(SDIR)/scythe.h
+-test.o: $(SDIR)/scythe.h
+ 
+-valgrind: build
++# special case, source is not ./src/tests.c
++tests.o: $(SDIR)/scythe.h src/tests/tests.c
++	$(CC) $(CFLAGS) -c src/tests/tests.c -o $@
++
++valgrind: scythe
+ 	valgrind --leak-check=full --show-reachable=yes ./scythe -a solexa_adapters.fa test.fastq
+ 
+-test: clean match.o util.o prob.o test.o
+-	$(CC) $(CFLAGS) $? -o test $(LDFLAGS) $(LDTESTFLAGS) && ./test
++test: test-scythe
++	./test-scythe
+ 
+ testclean:
+-	rm -rf ./tests
++	rm -rf ./tests ./test-scythe
+ 
+ clean:
+-	rm -rf *.o ./scythe *.dSYM
++	rm -rf *.o ./scythe ./test-scythe ./libscythe.so *.dSYM
+ 
+ distclean: clean
+ 	rm -rf *.tar.gz
+ 
+ dist:
+-	tar -zcf $(ARCHIVE).tar.gz src Makefile
++	tar -zcf $(ARCHIVE).tar.gz src Makefile illumina_adapters.fa
+ 
+-all: $(OBJS)
+-	$(CC) $(CFLAGS) $? -o scythe $(LDFLAGS)
+ 
+ lib: libscythe.so
+ 
+-libscythe.so: CFLAGS += -fpic
+ libscythe.so: $(LOBJS)
+ 	$(CC) $(CFLAGS) -shared -o $@ $^ $(LDFLAGS)
++
++debian:
++	mkdir -p scythe-debian
++	cp -r debian src Makefile illumina_adapters.fa scythe-debian
++	tar -zcf $(ARCHIVE).orig.tar.gz src Makefile illumina_adapters.fa
++
++debian-clean:
++	rm -f scythe_*.deb scythe*.dsc scythe_*.build scythe_*.changes  scythe_*.debian.tar.*  scythe_*.orig.tar.gz
++	rm -rf scythe-debian
++	$(MAKE) clean distclean
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..d4b8d64
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+0001-Makefile-cleaning-for-debian.patch

-- 
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