Author: Michael R. Crusoe <crusoe@debian.org>
Description: Attempt to use the Debian package of SDSL, fails as SDSL hasn't released since 2016 and VG requires a snapshot from 2017
Forwarded: not-needed
--- vg.orig/Makefile
+++ vg/Makefile
@@ -173,7 +173,6 @@
 
 
 LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
-SDSL_DIR:=deps/sdsl-lite
 SNAPPY_DIR:=deps/snappy
 GCSA2_DIR:=deps/gcsa2
 GBWT_DIR:=deps/gbwt
@@ -209,7 +208,6 @@
 # But that requires fancy ar scripting.
 # If you just pass them to ar it puts the library *file* in libvg where nothing can read it.
 LIB_DEPS =
-LIB_DEPS += $(LIB_DIR)/libsdsl.a
 LIB_DEPS += $(LIB_DIR)/libssw.a
 LIB_DEPS += $(LIB_DIR)/libsnappy.a
 LIB_DEPS += $(LIB_DIR)/libgcsa2.a
@@ -289,14 +287,6 @@
 test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp
 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(FILTER)
 
-$(LIB_DIR)/libsdsl.a: $(SDSL_DIR)/lib/*.cpp $(SDSL_DIR)/include/sdsl/*.hpp
-ifeq ($(shell uname -s),Darwin)
-	+. ./source_me.sh && cd $(SDSL_DIR) && AS_INTEGRATED_ASSEMBLER=1 BUILD_PORTABLE=1 ./install.sh $(CWD) $(FILTER)
-else
-	+. ./source_me.sh && cd $(SDSL_DIR) && BUILD_PORTABLE=1 ./install.sh $(CWD) $(FILTER)
-endif	
-
-
 $(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(SSW_DIR)/*.h
 	+. ./source_me.sh && cd $(SSW_DIR) && $(MAKE) $(FILTER) && ar rs $(CWD)/$(LIB_DIR)/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h $(CWD)/$(LIB_DIR)
 
@@ -305,7 +295,7 @@
 
 $(INC_DIR)/gcsa/gcsa.h: $(LIB_DIR)/libgcsa2.a
 
-$(LIB_DIR)/libgcsa2.a: $(LIB_DIR)/libsdsl.a $(wildcard $(GCSA2_DIR)/*.cpp) $(wildcard $(GCSA2_DIR)/include/gcsa/*.h)
+$(LIB_DIR)/libgcsa2.a: $(wildcard $(GCSA2_DIR)/*.cpp) $(wildcard $(GCSA2_DIR)/include/gcsa/*.h)
 ifeq ($(shell uname -s),Darwin)
 	+. ./source_me.sh && cd $(GCSA2_DIR) && AS_INTEGRATED_ASSEMBLER=1 $(MAKE) libgcsa2.a $(FILTER) && mv libgcsa2.a $(CWD)/$(LIB_DIR) && cp -r include/gcsa $(CWD)/$(INC_DIR)/
 else
@@ -313,7 +303,7 @@
 endif
 
 $(INC_DIR)/gbwt/dynamic_gbwt.h: $(LIB_DIR)/libgbwt.a
-$(LIB_DIR)/libgbwt.a: $(LIB_DIR)/libsdsl.a $(wildcard $(GBWT_DIR)/*.cpp) $(wildcard $(GBWT_DIR)/include/gbwt/*.h)
+$(LIB_DIR)/libgbwt.a: $(wildcard $(GBWT_DIR)/*.cpp) $(wildcard $(GBWT_DIR)/include/gbwt/*.h)
 ifeq ($(shell uname -s),Darwin)
 	+. ./source_me.sh && cd $(GBWT_DIR) && AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && mv libgbwt.a $(CWD)/$(LIB_DIR) && cp -r include/gbwt $(CWD)/$(INC_DIR)/
 else
@@ -433,7 +423,7 @@
 $(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp $(LIB_DIR)/libhts.a
 	cd $(LINLS_DIR) && $(MAKE) clean && INCLUDE_FLAGS="-I$(CWD)/$(INC_DIR)" $(MAKE) libs $(FILTER) && cp lib/libsublinearLS.a $(CWD)/$(LIB_DIR)/ && mkdir -p $(CWD)/$(INC_DIR)/sublinearLS && cp src/*.hpp $(CWD)/$(INC_DIR)/sublinearLS/
 
-$(LIB_DIR)/libbdsg.a: $(LIBBDSG_DIR)/src/*.cpp $(LIBBDSG_DIR)/include/bdsg/*.hpp $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/libsdsl.a $(INC_DIR)/sparsepp/spp.h
+$(LIB_DIR)/libbdsg.a: $(LIBBDSG_DIR)/src/*.cpp $(LIBBDSG_DIR)/include/bdsg/*.hpp $(LIB_DIR)/libhandlegraph.a $(INC_DIR)/sparsepp/spp.h
 	cd $(LIBBDSG_DIR) && CPLUS_INCLUDE_PATH=$(CWD)/$(INC_DIR):$(CPLUS_INCLUDE_PATH) make && cp lib/libbdsg.a $(CWD)/$(LIB_DIR) && pwd && cp -r include/bdsg $(CWD)/$(INC_DIR)
 
 # Auto-git-versioning
@@ -569,7 +559,6 @@
 	cd $(DEP_DIR) && cd gssw && $(MAKE) clean
 	cd $(DEP_DIR) && cd ssw && cd src && $(MAKE) clean
 	cd $(DEP_DIR) && cd progress_bar && $(MAKE) clean
-	cd $(DEP_DIR) && cd sdsl-lite && ./uninstall.sh || true
 	cd $(DEP_DIR) && cd libVCFH && $(MAKE) clean
 	cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
 	cd $(DEP_DIR) && cd gfakluge && $(MAKE) clean
--- vg.orig/deps/gbwt/Makefile
+++ vg/deps/gbwt/Makefile
@@ -1,9 +1,9 @@
-SDSL_DIR=../sdsl-lite
-include $(SDSL_DIR)/Make.helper
+INC_DIR=/usr/include/sdsl
+MY_CXX=c++
 
 # Multithreading with OpenMP.
 PARALLEL_FLAGS=-fopenmp -pthread
-LIBS=-L$(LIB_DIR) -lsdsl -ldivsufsort -ldivsufsort64
+LIBS=-lsdsl -ldivsufsort -ldivsufsort64
 
 ifeq ($(shell uname -s),Darwin)
     # Our compiler might be clang that lacks -fopenmp support.
@@ -32,7 +32,7 @@
 
 OTHER_FLAGS=$(PARALLEL_FLAGS)
 
-CXX_FLAGS=$(MY_CXX_FLAGS) $(OTHER_FLAGS) $(MY_CXX_OPT_FLAGS) -I$(INC_DIR) -Iinclude
+CXX_FLAGS+=$(MY_CXX_FLAGS) $(OTHER_FLAGS) $(MY_CXX_OPT_FLAGS) -I$(INC_DIR) -Iinclude
 LIBOBJS=algorithms.o bwtmerge.o dynamic_gbwt.o files.o gbwt.o internal.o metadata.o support.o utils.o variants.o
 SOURCES=$(wildcard *.cpp)
 HEADERS=$(wildcard include/gbwt/*.h)
--- vg.orig/deps/gcsa2/Makefile
+++ vg/deps/gcsa2/Makefile
@@ -1,5 +1,5 @@
-SDSL_DIR=../sdsl-lite
-include $(SDSL_DIR)/Make.helper
+INC_DIR=/usr/include/sdsl
+MY_CXX=g++
 
 # This enables various debugging options in build_gcsa.
 #VERIFY_FLAGS=-DVERIFY_CONSTRUCTION
