1 files changed, 0 insertions, 65 deletions
diff --git a/delly-use-system-libraries.patch b/delly-use-system-libraries.patch
deleted file mode 100644
index 3ce817f..0000000
--- a/delly-use-system-libraries.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-This patch let's Delly use the system versions of htslib and boost.
-
-Patch by Roel Janssen <roel@gnu.org>
---- a/Makefile	2016-03-16 13:08:49.936706607 +0100
-+++ b/Makefile	2016-03-16 13:09:12.351706212 +0100
-@@ -9,8 +9,8 @@
- 
- # Flags
- CXX=g++
--CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas
--LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
-+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas
-+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
- 
- # Additional flags for release/debug
- ifeq (${PARALLEL}, 1)
-@@ -23,7 +23,7 @@
- ifeq (${STATIC}, 1)
- 	LDFLAGS += -static -static-libgcc -pthread -lhts -lz
- else
--	LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib
-+	LDFLAGS += -lhts -lz
- endif
- ifeq (${DEBUG}, 1)
- 	CXXFLAGS += -g -O0 -fno-inline -DDEBUG
-@@ -41,32 +41,24 @@
- DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
- 
- # Targets
--TARGETS = .htslib .boost src/delly src/extract src/cov src/iover src/stats
-+TARGETS = src/delly src/extract src/cov src/iover src/stats
- 
- all:   	$(TARGETS)
- 
--.htslib: $(HTSLIBSOURCES)
--	cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
--
--.boost: $(BOOSTSOURCES)
--	cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost
--
--src/delly: .htslib .boost $(DELLYSOURCES)
-+src/delly: $(DELLYSOURCES)
- 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
- 
--src/extract: .htslib .boost $(DELLYSOURCES)
-+src/extract: $(DELLYSOURCES)
- 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
- 
--src/cov: .htslib .boost $(DELLYSOURCES)
-+src/cov: $(DELLYSOURCES)
- 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
- 
--src/iover: .htslib .boost $(DELLYSOURCES)
-+src/iover: $(DELLYSOURCES)
- 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
- 
--src/stats: .htslib .boost $(DELLYSOURCES)
-+src/stats: $(DELLYSOURCES)
- 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
- 
- clean:
--	cd src/htslib && make clean
--	cd src/modular-boost && ./b2 --clean-all
--	rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost
-+	rm -f $(TARGETS) $(TARGETS:=.o)