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commit c9ab57aa0cdb1471ecba50c062f09f8dcd6fab3c Author: Kevin Murray <s...@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 <s...@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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/scythe.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit