diff --git a/.github/workflows/testmac.yml b/.github/workflows/testmac.yml
index 11d656e7a05..802d656ccfb 100644
--- a/.github/workflows/testmac.yml
+++ b/.github/workflows/testmac.yml
@@ -15,7 +15,7 @@ on:
 jobs:
   testmac:
     name: Test on Mac
-    runs-on: macos-12
+    runs-on: macos-15
 
     steps:
       - name: Use cache
@@ -26,14 +26,14 @@ jobs:
             lib
             include
             bin
-          key: ${{ runner.os }}-12-${{ github.ref }}
+          key: ${{ runner.os }}-15-${{ github.ref }}
           # Restore keys are a "list", but really only a multiline string is
           # accepted. Also we match by prefix. And the most recent cache is
           # used, not the most specific.
           # See: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key
           restore-keys: |
-            ${{ runner.os }}-12-${{ github.base_ref }}
-            ${{ runner.os }}-12
+            ${{ runner.os }}-15-${{ github.base_ref }}
+            ${{ runner.os }}-15
           
       - name: Checkout code without submodules
         uses: actions/checkout@v2
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 65d745c2e2b..3fbdc26907a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -86,8 +86,6 @@ local-build-test-job:
   script:
     - THREADS=8
     - nvm version
-    - python3 ./configure.py
-    - source ./source_me.sh
     - make get-deps
     - make -j${THREADS}
     - echo Testing
@@ -96,6 +94,8 @@ local-build-test-job:
     - make test
     - make static -j${THREADS}
     # Also test as a backend for the tube map
+    # Tube map expects vg on PATH
+    - export PATH="$(pwd)/bin:${PATH}"
     - git clone https://github.com/vgteam/sequenceTubeMap.git
     - cd sequenceTubeMap
     # Tube map expects local IPv6 but Kubernetes won't let us have it
diff --git a/Dockerfile b/Dockerfile
index ff1433eccfc..cf4279d6045 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -48,7 +48,6 @@ RUN apt-get -qq -y update && apt-get -qq -y upgrade && apt-get -qq -y install \
 ###DEPS_END###
 
 # Prepare to build submodule dependencies
-COPY source_me.sh /vg/source_me.sh
 COPY deps /vg/deps
 # To increase portability of the docker image, when building for amd64, set the
 # target CPU architecture to Nehalem (2008) rather than auto-detecting the
@@ -59,17 +58,17 @@ RUN if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then sed -i s/m
 RUN find . -name CMakeCache.txt | xargs rm -f
 # Build the dependencies
 COPY Makefile /vg/Makefile
-RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" CFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
+RUN CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" CFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
 
 # Bring in the sources, which we need in order to build.
 COPY src /vg/src
 
 # Build all the object files for vg, but don't link.
 # Also pass the arch here
-RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) objs
+RUN CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) objs
 
 # Do the final build and link, knowing the version. Trim down the resulting binary but make sure to include enough debug info for profiling.
-RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
+RUN CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
 
 # Ship the scripts
 COPY scripts /vg/scripts
diff --git a/Makefile b/Makefile
index 67c1e556f0e..b2f25faaffc 100644
--- a/Makefile
+++ b/Makefile
@@ -22,12 +22,14 @@ LIB_DIR:=lib
 # INC_DIR must be a relative path
 INC_DIR:=include
 CWD:=$(shell pwd)
-CXX ?= g++
 PKG_CONFIG ?= pkg-config
 
 SFX :=
 EXE:=vg$(SFX)
 
+# Expose compiler we want to use to all build commands as an environment variable.
+export CC CXX
+
 all: $(BIN_DIR)/$(EXE)
 
 # Magic dependencies (see <http://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#tldr>)
@@ -494,12 +496,12 @@ $(LIB_DIR)/libvg.$(SHARED_SUFFIX): $(LIBVG_SHARED_DEPS)
 
 # Each test set can have its own binary, and not link everything static
 $(UNITTEST_EXE): $(UNITTEST_BIN_DIR)/%: $(UNITTEST_OBJ_DIR)/%.o $(UNITTEST_SUPPORT_OBJ) $(CONFIG_OBJ) $(LIB_DIR)/libvg.$(SHARED_SUFFIX)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(UNITTEST_SUPPORT_OBJ) $(CONFIG_OBJ) $(LIB_DIR)/libvg.$(SHARED_SUFFIX) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LD_LIB_FLAGS) $(LD_STATIC_LIB_FLAGS) $(LD_STATIC_LIB_DEPS) $(LD_EXE_LIB_FLAGS)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(UNITTEST_SUPPORT_OBJ) $(CONFIG_OBJ) $(LIB_DIR)/libvg.$(SHARED_SUFFIX) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LD_LIB_FLAGS) $(LD_STATIC_LIB_FLAGS) $(LD_STATIC_LIB_DEPS) $(LD_EXE_LIB_FLAGS)
 
 # For a normal dynamic build we remove the static build marker
 $(BIN_DIR)/$(EXE): $(LIB_DIR)/libvg.a $(EXE_DEPS)
 	-rm -f $(LIB_DIR)/vg_is_static
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(LD_STATIC_LIB_DEPS) $(LD_EXE_LIB_FLAGS)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(LD_STATIC_LIB_DEPS) $(LD_EXE_LIB_FLAGS)
 # We keep a file that we touch on the last static build.
 # If the vg linkables are newer than the last static build, we do a build
 $(LIB_DIR)/vg_is_static: $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(DEPS) $(LINK_DEPS)
@@ -521,16 +523,15 @@ static-docker: static scripts/*
 # We have system-level deps to install
 # We want the One True Place for them to be in the Dockerfile.
 get-deps:
-	sudo apt-get install -qq -y --no-upgrade $(shell cat Dockerfile | sed -n '/^###DEPS_BEGIN###/,$${p;/^###DEPS_END###/q}' | grep -v '^ *#' | grep -v "^RUN" | tr '\n' ' ' | tr -d '\\')
+	sudo DEBIAN_FRONTEND=$(DEBIAN_FRONTEND) apt-get install -qq -y --no-upgrade $(shell cat Dockerfile | sed -n '/^###DEPS_BEGIN###/,$${p;/^###DEPS_END###/q}' | grep -v '^ *#' | grep -v "^RUN" | tr '\n' ' ' | tr -d '\\')
 
 # And we have submodule deps to build
 deps: $(DEPS)
 
 test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BIN_DIR)/vcf2tsv $(FASTAHACK_DIR)/fastahack $(BIN_DIR)/rapper
-	. ./source_me.sh && cd test && prove -v t
+	cd test && prove -v t
 	# Hide the compiler configuration from the doc tests, so that the ones that
-	# build code can't pick up libraries out of the bg build itself. Definitely
-	# don't source source_me.sh!
+	# build code can't pick up libraries out of the vg build itself.
 	# But still supply vg on the PATH. Hope it knows where its own libraries are.
 	CFLAGS= CXXFLAGS= CPPFLAGS= LDFLAGS= INCLUDE_FLAGS= LIBRARY_PATH= LD_LIBRARY_PATH= DYLD_LIBRARY_PATH= DYLD_FALLBACK_LIBRARY_PATH= LD_INCLUDE_PATH= CC= CXX= CXX_STANDARD= PATH=$(CWD)/bin:$(PATH) doc/test-docs.sh
 
@@ -557,67 +558,67 @@ else
 endif
 
 test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/vg.hpp
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(FILTER)
 
 # TODO: The normal and debug jemalloc builds can't safely be run at the same time.
 $(LIB_DIR)/libjemalloc.a: $(JEMALLOC_DIR)/src/*.c
-	+. ./source_me.sh && rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/ && cp -r include/* $(CWD)/$(INC_DIR)/
+	+rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/ && cp -r include/* $(CWD)/$(INC_DIR)/
 
 $(LIB_DIR)/libjemalloc_debug.a: $(JEMALLOC_DIR)/src/*.c
-	+. ./source_me.sh && rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --enable-debug --enable-fill --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/libjemalloc_debug.a && cp -r include/* $(CWD)/$(INC_DIR)/
+	+rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --enable-debug --enable-fill --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/libjemalloc_debug.a && cp -r include/* $(CWD)/$(INC_DIR)/
 
 # Use fake patterns to tell Make that this rule generates all these files when run once.
 # Here % should always match "lib" which is a common substring.
 # See https://stackoverflow.com/a/19822767
 $(LIB_DIR)/%sdsl.a $(LIB_DIR)/%divsufsort.a $(LIB_DIR)/%divsufsort64.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 CXXFLAGS="-fPIC $(CPPFLAGS) $(CXXFLAGS)" ./install.sh $(CWD) $(FILTER)
+	+cd $(SDSL_DIR) && AS_INTEGRATED_ASSEMBLER=1 BUILD_PORTABLE=1 CXXFLAGS="-fPIC $(CPPFLAGS) $(CXXFLAGS)" ./install.sh $(CWD) $(FILTER)
 else
-	+. ./source_me.sh && cd $(SDSL_DIR) && BUILD_PORTABLE=1 CXXFLAGS="-fPIC $(CPPFLAGS) $(CXXFLAGS)" ./install.sh $(CWD) $(FILTER)
+	+cd $(SDSL_DIR) && BUILD_PORTABLE=1 CXXFLAGS="-fPIC $(CPPFLAGS) $(CXXFLAGS)" ./install.sh $(CWD) $(FILTER)
 endif
 
 $(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(SSW_DIR)/*.cpp $(SSW_DIR)/*.h
-	+. ./source_me.sh && cd $(SSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && ar rs $(CWD)/$(LIB_DIR)/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h $(CWD)/$(INC_DIR)
+	+cd $(SSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && ar rs $(CWD)/$(LIB_DIR)/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h $(CWD)/$(INC_DIR)
 
 # We need to hide -Xpreprocessor -fopenmp from Snappy, at least on Mac, because
 # it will drop the -Xpreprocessor and keep the -fopenmp and upset Clang.
 $(LIB_DIR)/libsnappy.a: $(SNAPPY_DIR)/*.cc $(SNAPPY_DIR)/*.h
-	+. ./source_me.sh && cd $(SNAPPY_DIR) && ./autogen.sh && CXXFLAGS="-fPIC $(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./configure --prefix=$(CWD) $(FILTER) && CXXFLAGS="-fPIC $(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) libsnappy.la $(FILTER) && cp .libs/libsnappy.a $(CWD)/lib/ && cp snappy-c.h snappy-sinksource.h snappy-stubs-public.h snappy.h $(CWD)/include/
+	+cd $(SNAPPY_DIR) && ./autogen.sh && CXXFLAGS="-fPIC $(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./configure --prefix=$(CWD) $(FILTER) && CXXFLAGS="-fPIC $(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) libsnappy.la $(FILTER) && cp .libs/libsnappy.a $(CWD)/lib/ && cp snappy-c.h snappy-sinksource.h snappy-stubs-public.h snappy.h $(CWD)/include/
 
 $(INC_DIR)/gcsa/gcsa.h: $(LIB_DIR)/libgcsa2.a
 
 $(LIB_DIR)/libgcsa2.a: $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(wildcard $(GCSA2_DIR)/*.cpp) $(wildcard $(GCSA2_DIR)/include/gcsa/*.h)
 ifeq ($(shell uname -s),Darwin)
-	+. ./source_me.sh && cp -r $(GCSA2_DIR)/include/gcsa $(CWD)/$(INC_DIR)/ && cd $(GCSA2_DIR) && $(MAKE) clean && make directories && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) lib/libgcsa2.a $(FILTER) && mv lib/libgcsa2.a $(CWD)/$(LIB_DIR)
+	+cp -r $(GCSA2_DIR)/include/gcsa $(CWD)/$(INC_DIR)/ && cd $(GCSA2_DIR) && $(MAKE) clean && make directories && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) lib/libgcsa2.a $(FILTER) && mv lib/libgcsa2.a $(CWD)/$(LIB_DIR)
 else
-	+. ./source_me.sh && cp -r $(GCSA2_DIR)/include/gcsa $(CWD)/$(INC_DIR)/ && cd $(GCSA2_DIR) && $(MAKE) clean && make directories && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) lib/libgcsa2.a $(FILTER) && mv lib/libgcsa2.a $(CWD)/$(LIB_DIR)
+	+cp -r $(GCSA2_DIR)/include/gcsa $(CWD)/$(INC_DIR)/ && cd $(GCSA2_DIR) && $(MAKE) clean && make directories && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) lib/libgcsa2.a $(FILTER) && mv lib/libgcsa2.a $(CWD)/$(LIB_DIR)
 endif
 
 $(INC_DIR)/gbwt/dynamic_gbwt.h: $(LIB_DIR)/libgbwt.a
 
 $(LIB_DIR)/libgbwt.a: $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(wildcard $(GBWT_DIR)/src/*.cpp) $(wildcard $(GBWT_DIR)/include/gbwt/*.h)
 ifeq ($(shell uname -s),Darwin)
-	+. ./source_me.sh && cp -r $(GBWT_DIR)/include/gbwt $(CWD)/$(INC_DIR)/ && cd $(GBWT_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && mv lib/libgbwt.a $(CWD)/$(LIB_DIR)
+	+cp -r $(GBWT_DIR)/include/gbwt $(CWD)/$(INC_DIR)/ && cd $(GBWT_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && mv lib/libgbwt.a $(CWD)/$(LIB_DIR)
 else
-	+. ./source_me.sh && cp -r $(GBWT_DIR)/include/gbwt $(CWD)/$(INC_DIR)/ && cd $(GBWT_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && mv lib/libgbwt.a $(CWD)/$(LIB_DIR)
+	+cp -r $(GBWT_DIR)/include/gbwt $(CWD)/$(INC_DIR)/ && cd $(GBWT_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && mv lib/libgbwt.a $(CWD)/$(LIB_DIR)
 endif
 
 $(INC_DIR)/gbwtgraph/gbwtgraph.h: $(LIB_DIR)/libgbwtgraph.a
 
 $(LIB_DIR)/libgbwtgraph.a: $(LIB_DIR)/libgbwt.a $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(LIB_DIR)/libhandlegraph.a $(wildcard $(GBWTGRAPH_DIR)/src/*.cpp) $(wildcard $(GBWTGRAPH_DIR)/include/gbwtgraph/*.h)
 ifeq ($(shell uname -s),Darwin)
-	+. ./source_me.sh && cp -r $(GBWTGRAPH_DIR)/include/gbwtgraph $(CWD)/$(INC_DIR)/ && cd $(GBWTGRAPH_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && mv lib/libgbwtgraph.a $(CWD)/$(LIB_DIR)
+	+cp -r $(GBWTGRAPH_DIR)/include/gbwtgraph $(CWD)/$(INC_DIR)/ && cd $(GBWTGRAPH_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && mv lib/libgbwtgraph.a $(CWD)/$(LIB_DIR)
 else
-	+. ./source_me.sh && cp -r $(GBWTGRAPH_DIR)/include/gbwtgraph $(CWD)/$(INC_DIR)/ && cd $(GBWTGRAPH_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && mv lib/libgbwtgraph.a $(CWD)/$(LIB_DIR)
+	+cp -r $(GBWTGRAPH_DIR)/include/gbwtgraph $(CWD)/$(INC_DIR)/ && cd $(GBWTGRAPH_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && mv lib/libgbwtgraph.a $(CWD)/$(LIB_DIR)
 endif
 
 $(INC_DIR)/kff_io.hpp: $(LIB_DIR)/libkff.a
 
 $(LIB_DIR)/libkff.a: $(KFF_DIR)/kff_io.cpp $(KFF_DIR)/kff_io.hpp.in
 ifeq ($(shell uname -s),Darwin)
-	+. ./source_me.sh && cd $(KFF_DIR) && rm -Rf build && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS="-fPIC -Wall -Ofast -g $(CXXFLAGS)" .. && AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && cp kff_io.hpp $(CWD)/$(INC_DIR) && mv libkff.a $(CWD)/$(LIB_DIR)
+	+cd $(KFF_DIR) && rm -Rf build && mkdir build && cd build && cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_CXX_FLAGS="-fPIC -Wall -Ofast -g $(CXXFLAGS)" .. && AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && cp kff_io.hpp $(CWD)/$(INC_DIR) && mv libkff.a $(CWD)/$(LIB_DIR)
 else
-	+. ./source_me.sh && cd $(KFF_DIR) && rm -Rf build && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS="-fPIC -Wall -Ofast -g $(CXXFLAGS)" .. && $(MAKE) $(FILTER) && cp kff_io.hpp $(CWD)/$(INC_DIR) && mv libkff.a $(CWD)/$(LIB_DIR)
+	+cd $(KFF_DIR) && rm -Rf build && mkdir build && cd build && cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_CXX_FLAGS="-fPIC -Wall -Ofast -g $(CXXFLAGS)" .. && $(MAKE) $(FILTER) && cp kff_io.hpp $(CWD)/$(INC_DIR) && mv libkff.a $(CWD)/$(LIB_DIR)
 endif
 
 $(INC_DIR)/BooPHF.h: $(BBHASH_DIR)/BooPHF.h
@@ -627,17 +628,17 @@ $(INC_DIR)/progress_bar.hpp: $(PROGRESS_BAR_DIR)/progress_bar.hpp
 	+cp $(PROGRESS_BAR_DIR)/progress_bar.hpp $(CWD)/$(INC_DIR)
 
 $(OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/progress_bar.cpp $(PROGRESS_BAR_DIR)/*.hpp
-	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $<
+	+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $<
 $(SHARED_OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/progress_bar.cpp $(PROGRESS_BAR_DIR)/*.hpp
-	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
+	+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
 
 $(INC_DIR)/Fasta.h:  $(FASTAHACK_DIR)/Fasta.h
-	+. ./source_me.sh && cd $(FASTAHACK_DIR) && cp Fasta.h $(CWD)/$(INC_DIR)
+	+cd $(FASTAHACK_DIR) && cp Fasta.h $(CWD)/$(INC_DIR)
 
 $(OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h 
-	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
+	+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
 $(SHARED_OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h
-	+. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
+	+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
 
 # We have this target to clean up the old Protobuf we used to have.
 # We can remove it after we no longer care about building properly on a dirty
@@ -663,10 +664,10 @@ $(LIB_DIR)/cleaned_old_elfutils:
 $(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIB_DIR)/cleaned_old_protobuf_v003 $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp $(LIBVGIO_DIR)/deps/vg.proto
 	+rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h
 	+rm -Rf $(CWD)/$(INC_DIR)/vg/io/
-	+. ./source_me.sh && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && export LDFLAGS="$(LD_LIB_DIR_FLAGS) $(LDFLAGS)" && cd $(LIBVGIO_DIR) && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_CXX_STANDARD=$(CXX_STANDARD) -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install
+	+export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && export LDFLAGS="$(LD_LIB_DIR_FLAGS) $(LDFLAGS)" && cd $(LIBVGIO_DIR) && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_CXX_STANDARD=$(CXX_STANDARD) -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install
 
 $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLEGRAPH_DIR)/src/include/handlegraph/*.hpp $(LIBHANDLEGRAPH_DIR)/src/*.cpp
-	+. ./source_me.sh && cd $(LIBHANDLEGRAPH_DIR) && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="$(CXXFLAGS) $(CPPFLAGS)" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. && $(MAKE) $(FILTER) && $(MAKE) install
+	+cd $(LIBHANDLEGRAPH_DIR) && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="$(CXXFLAGS) $(CPPFLAGS)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. && $(MAKE) $(FILTER) && $(MAKE) install
 
 
 # On Linux, libdeflate builds a .so.
@@ -682,7 +683,7 @@ ifeq ($(shell uname -s),Darwin)
 endif
 
 $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDEFLATE_DIR)/lib/*/*.h $(LIBDEFLATE_DIR)/lib/*.c $(LIBDEFLATE_DIR)/lib/*/*.c
-	+. ./source_me.sh && cd $(LIBDEFLATE_DIR) && V=1 LDFLAGS="$(LDFLAGS) $(LD_RENAMEABLE_FLAGS)" $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
+	+cd $(LIBDEFLATE_DIR) && V=1 LDFLAGS="$(LDFLAGS) $(LD_RENAMEABLE_FLAGS)" $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
 
 # We build htslib after libdeflate so it can use libdeflate.
 # We need to do some wizardry to get it to pick up the right build and target system types on modern autotools.
@@ -695,13 +696,13 @@ $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDE
 # a system path, in case another htslib is installed on the system. Some HTSlib
 # headers look for the current HTSlib with <>.
 $(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc $(LIB_DIR)/libhts%$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
-	+. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoreconf -i && autoheader && autoconf || true
-	+. ./source_me.sh && cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
-	+. ./source_me.sh && cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
+	+cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoreconf -i && autoheader && autoconf || true
+	+cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
+	+cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
 
 # Build and install tabixpp for vcflib.
 $(LIB_DIR)/libtabixpp.a: $(LIB_DIR)/libhts.a $(TABIXPP_DIR)/*.cpp $(TABIXPP_DIR)/*.hpp
-	+. ./source_me.sh && cd $(TABIXPP_DIR) && rm -f tabix.o libtabixpp.a && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_HEADERS="" $(MAKE) tabix.o $(FILTER) && ar rcs libtabixpp.a tabix.o
+	+cd $(TABIXPP_DIR) && rm -f tabix.o libtabixpp.a && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_HEADERS="" $(MAKE) tabix.o $(FILTER) && ar rcs libtabixpp.a tabix.o
 	+cp $(TABIXPP_DIR)/libtabixpp.a $(LIB_DIR) && cp $(TABIXPP_DIR)/tabix.hpp $(INC_DIR)
 	+echo "Name: tabixpp" > $(LIB_DIR)/pkgconfig/tabixpp.pc
 	+echo "Description: Self-packaged tabixpp" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
@@ -717,7 +718,7 @@ $(LIB_DIR)/libtabixpp.a: $(LIB_DIR)/libhts.a $(TABIXPP_DIR)/*.cpp $(TABIXPP_DIR)
 # We need to use /usr first for CMake search or Ubuntu 22.04 will decide pybind11 is installed in / when actually it is only fully installed in /usr.
 $(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libtabixpp.a $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.hpp $(VCFLIB_DIR)/contrib/*/*.cpp $(VCFLIB_DIR)/contrib/*/*.h
 	+rm -f $(VCFLIB_DIR)/contrib/WFA2-lib/VERSION
-	+. ./source_me.sh && cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" .. && cmake --build .
+	+cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" .. && cmake --build .
 	+cp $(VCFLIB_DIR)/contrib/filevercmp/*.h* $(INC_DIR)
 	+cp $(VCFLIB_DIR)/contrib/fastahack/*.h* $(INC_DIR)
 	+cp $(VCFLIB_DIR)/contrib/smithwaterman/*.h* $(INC_DIR)
@@ -731,10 +732,10 @@ $(BIN_DIR)/vcf2tsv: $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.h $(LIB_DIR)/lib
 	+cp $(VCFLIB_DIR)/build/vcf2tsv $(BIN_DIR)
 
 $(FASTAHACK_DIR)/fastahack: $(FASTAHACK_DIR)/*.c $(FASTAHACK_DIR)/*.h $(FASTAHACK_DIR)/*.cpp
-	+. ./source_me.sh && cd $(FASTAHACK_DIR) && $(MAKE) $(FILTER)
+	+cd $(FASTAHACK_DIR) && $(MAKE) $(FILTER)
 
 $(LIB_DIR)/libgssw.a: $(GSSW_DIR)/src/gssw.c $(GSSW_DIR)/src/gssw.h
-	+. ./source_me.sh && cd $(GSSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
+	+cd $(GSSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
 
 $(INC_DIR)/lru_cache.h: $(DEP_DIR)/lru_cache/*.h $(DEP_DIR)/lru_cache/*.cc
 	+cd $(DEP_DIR)/lru_cache && cp *.h* $(CWD)/$(INC_DIR)/
@@ -743,32 +744,32 @@ $(INC_DIR)/lru_cache.h: $(DEP_DIR)/lru_cache/*.h $(DEP_DIR)/lru_cache/*.cc
 $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/dynamic/*.hpp $(DYNAMIC_DIR)/include/dynamic/*/*.hpp
 	+rm -Rf $(INC_DIR)/dynamic.hpp $(INC_DIR)/dynamic
 	# annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers
-	+cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make && cp -r $(CWD)/$(DYNAMIC_DIR)/deps/hopscotch_map/include/* $(CWD)/$(INC_DIR)/
+	+cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE=ON .. && make && cp -r $(CWD)/$(DYNAMIC_DIR)/deps/hopscotch_map/include/* $(CWD)/$(INC_DIR)/
 	# Do the copy of the main file last so we can tell if this recipe failed and redo it.
 	# Otherwise we get dynamic.hpp without its deps
 	+mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/dynamic/* $(INC_DIR)/dynamic/
 
 $(INC_DIR)/sparsehash/sparse_hash_map: $(wildcard $(SPARSEHASH_DIR)/**/*.cc) $(wildcard $(SPARSEHASH_DIR)/**/*.h)
-	+. ./source_me.sh && cd $(SPARSEHASH_DIR) && ./autogen.sh && LDFLAGS="$(LD_LIB_DIR_FLAGS) $(LDFLAGS)" ./configure --prefix=$(CWD) $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install
+	+cd $(SPARSEHASH_DIR) && ./autogen.sh && LDFLAGS="$(LD_LIB_DIR_FLAGS) $(LDFLAGS)" ./configure --prefix=$(CWD) $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install
 
 $(INC_DIR)/sparsepp/spp.h: $(wildcard $(SPARSEHASH_DIR)/sparsepp/*.h)
 	+cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
 
 #$(INC_DIR)/Variant.h
 $(LIB_DIR)/libvcfh.a: $(DEP_DIR)/libVCFH/*.cpp $(DEP_DIR)/libVCFH/*.hpp
-	+. ./source_me.sh && cd $(DEP_DIR)/libVCFH && $(MAKE) $(FILTER) && cp libvcfh.a $(CWD)/$(LIB_DIR)/ && cp vcfheader.hpp $(CWD)/$(INC_DIR)/
+	+cd $(DEP_DIR)/libVCFH && $(MAKE) $(FILTER) && cp libvcfh.a $(CWD)/$(LIB_DIR)/ && cp vcfheader.hpp $(CWD)/$(INC_DIR)/
 
 $(LIB_DIR)/libsonlib.a: $(CWD)/$(DEP_DIR)/sonLib/C/inc/*.h $(CWD)/$(DEP_DIR)/sonLib/C/impl/*.c
-	+. ./source_me.sh && cd $(DEP_DIR)/sonLib && $(MAKE) clean && kyotoTycoonLib="" CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/sonLib.a $(CWD)/$(LIB_DIR)/libsonlib.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
+	+cd $(DEP_DIR)/sonLib && $(MAKE) clean && kyotoTycoonLib="" CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/sonLib.a $(CWD)/$(LIB_DIR)/libsonlib.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
 
 $(LIB_DIR)/libpinchesandcacti.a: $(LIB_DIR)/libsonlib.a $(CWD)/$(DEP_DIR)/pinchesAndCacti/inc/*.h $(CWD)/$(DEP_DIR)/pinchesAndCacti/impl/*.c
-	+. ./source_me.sh && cd $(DEP_DIR)/pinchesAndCacti && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cd $(CWD)/$(DEP_DIR)/sonLib && cp lib/stPinchesAndCacti.a $(CWD)/$(LIB_DIR)/libpinchesandcacti.a && cp lib/3EdgeConnected.a $(CWD)/$(LIB_DIR)/lib3edgeconnected.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
+	+cd $(DEP_DIR)/pinchesAndCacti && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cd $(CWD)/$(DEP_DIR)/sonLib && cp lib/stPinchesAndCacti.a $(CWD)/$(LIB_DIR)/libpinchesandcacti.a && cp lib/3EdgeConnected.a $(CWD)/$(LIB_DIR)/lib3edgeconnected.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
 
 # When building raptor we need to make sure to pre-generate and fix up the lexer
 # We also need to clear out its cmake stuff in case it found a wrong Bison and cached it.
 $(LIB_DIR)/libraptor2.a: $(RAPTOR_DIR)/src/* $(wildcard $(RAPTOR_DIR)/build/*)
 	which bison
-	+. ./source_me.sh && cd $(RAPTOR_DIR)/build && rm -Rf CMakeCache.txt CMakeFiles CTestTestfile.cmake Makefile cmake_install.cmake src tests utils && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" cmake .. && rm -f src/turtle_parser.c && rm -f src/turtle_lexer.c && make turtle_lexer_tgt && make -f src/CMakeFiles/raptor2.dir/build.make src/turtle_lexer.c && sed -i.bak '/yycleanup/d' src/turtle_lexer.c && $(MAKE) $(FILTER) && cp src/libraptor2.a $(CWD)/$(LIB_DIR)
+	+cd $(RAPTOR_DIR)/build && rm -Rf CMakeCache.txt CMakeFiles CTestTestfile.cmake Makefile cmake_install.cmake src tests utils && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" .. && rm -f src/turtle_parser.c && rm -f src/turtle_lexer.c && make turtle_lexer_tgt && make -f src/CMakeFiles/raptor2.dir/build.make src/turtle_lexer.c && sed -i.bak '/yycleanup/d' src/turtle_lexer.c && $(MAKE) $(FILTER) && cp src/libraptor2.a $(CWD)/$(LIB_DIR)
 	+touch $(LIB_DIR)/libraptor2.a
 
 # We need rapper from Raptor for the tests
@@ -782,7 +783,7 @@ $(INC_DIR)/raptor2/raptor2.h: $(LIB_DIR)/libraptor2.a $(RAPTOR_DIR)/build/*
 	+touch $(INC_DIR)/raptor2/raptor2.h
 
 $(LIB_DIR)/libstructures.a: $(STRUCTURES_DIR)/src/include/structures/*.hpp $(STRUCTURES_DIR)/src/*.cpp $(STRUCTURES_DIR)/Makefile
-	+. ./source_me.sh && cd $(STRUCTURES_DIR) && $(MAKE) clean && $(MAKE) lib/libstructures.a $(FILTER) && cp lib/libstructures.a $(CWD)/$(LIB_DIR)/ && cp -r src/include/structures $(CWD)/$(INC_DIR)/
+	+cd $(STRUCTURES_DIR) && $(MAKE) clean && $(MAKE) lib/libstructures.a $(FILTER) && cp lib/libstructures.a $(CWD)/$(LIB_DIR)/ && cp -r src/include/structures $(CWD)/$(INC_DIR)/
 
 $(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
 	+cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
@@ -812,15 +813,15 @@ $(LIB_DIR)/libdwfl.a: $(LIB_DIR)/libelf.a
 # running on.
 $(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/libebl/*.c $(ELFUTILS_DIR)/libebl/*.h $(ELFUTILS_DIR)/libdw/*.c $(ELFUTILS_DIR)/libdw/*.h $(ELFUTILS_DIR)/libelf/*.c $(ELFUTILS_DIR)/libelf/*.h $(ELFUTILS_DIR)/src/*.c $(ELFUTILS_DIR)/src/*.h $(LIB_DIR)/cleaned_old_elfutils
 	+cd $(CWD)/$(INC_DIR)/ && rm -Rf elfutils gelf.h libelf.h dwarf.h libdwflP.h libdwfl.h libebl.h libelf.h
-	+. ./source_me.sh && cd $(ELFUTILS_DIR) && autoreconf -i -f && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" ./configure --enable-maintainer-mode --disable-libdebuginfod --disable-debuginfod --prefix=$(CWD) $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libelf && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libelf.a $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libebl && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libebl.a $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwfl && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libdwfl.a $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwelf && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libdwelf.a $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/lib && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libeu.a $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libcpu && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libcpu.a $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/backends && $(MAKE) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) libebl_backends.a $(FILTER)
-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libdw && $(MAKE) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) libdw.a known-dwarf.h $(FILTER)
+	+cd $(ELFUTILS_DIR) && autoreconf -i -f && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" ./configure --enable-maintainer-mode --disable-libdebuginfod --disable-debuginfod --prefix=$(CWD) $(FILTER)
+	+cd $(ELFUTILS_DIR)/libelf && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libelf.a $(FILTER)
+	+cd $(ELFUTILS_DIR)/libebl && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libebl.a $(FILTER)
+	+cd $(ELFUTILS_DIR)/libdwfl && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libdwfl.a $(FILTER)
+	+cd $(ELFUTILS_DIR)/libdwelf && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libdwelf.a $(FILTER)
+	+cd $(ELFUTILS_DIR)/lib && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libeu.a $(FILTER)
+	+cd $(ELFUTILS_DIR)/libcpu && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libcpu.a $(FILTER)
+	+cd $(ELFUTILS_DIR)/backends && $(MAKE) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) libebl_backends.a $(FILTER)
+	+cd $(ELFUTILS_DIR)/libdw && $(MAKE) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) libdw.a known-dwarf.h $(FILTER)
 	+cd $(ELFUTILS_DIR) && mkdir -p $(CWD)/$(INC_DIR)/elfutils && cp libdw/known-dwarf.h libdw/libdw.h libebl/libebl.h libelf/elf-knowledge.h version.h libdwfl/libdwfl.h libdwelf/libdwelf.h $(CWD)/$(INC_DIR)/elfutils && cp libelf/gelf.h libelf/libelf.h libdw/dwarf.h $(CWD)/$(INC_DIR) && cp libebl/libebl.a libdw/libdw.a libdwfl/libdwfl.a libdwelf/libdwelf.a libelf/libelf.a $(CWD)/$(LIB_DIR)/
 
 $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
@@ -829,30 +830,30 @@ $(SHARED_OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
 	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
 
 $(LIB_DIR)/libfml.a: $(FERMI_DIR)/*.h $(FERMI_DIR)/*.c
-	. ./source_me.sh && cd $(FERMI_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp *.h $(CWD)/$(INC_DIR)/ && cp libfml.a $(CWD)/$(LIB_DIR)/
+	cd $(FERMI_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp *.h $(CWD)/$(INC_DIR)/ && cp libfml.a $(CWD)/$(LIB_DIR)/
 
 # We don't need to hack the build to point at our htslib because sublinearLS gets its htslib from the include flags we set
 # But we do need to hack out the return type error to work around https://github.com/yoheirosen/sublinear-Li-Stephens/issues/6
 # TODO: This probably means actually calling some things in the library is unsafe!
 $(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp $(LIB_DIR)/libhts.a
-	. ./source_me.sh && cd $(LINLS_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(filter-out -Werror=return-type,$(CFLAGS))" CXXFLAGS="-fPIC $(filter-out -Werror=return-type,$(CXXFLAGS))" 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/
+	cd $(LINLS_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(filter-out -Werror=return-type,$(CFLAGS))" CXXFLAGS="-fPIC $(filter-out -Werror=return-type,$(CXXFLAGS))" 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: $(INC_DIR)/BooPHF.h $(LIBBDSG_DIR)/Makefile $(LIBBDSG_DIR)/bdsg/src/*.cpp $(LIBBDSG_DIR)/bdsg/include/bdsg/*.hpp $(LIBBDSG_DIR)/bdsg/include/bdsg/internal/*.hpp $(LIBBDSG_DIR)/bdsg/include/bdsg/overlays/*.hpp $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(INC_DIR)/sparsepp/spp.h $(INC_DIR)/dynamic/dynamic.hpp $(INC_DIR)/mio/mmap.hpp
-	+. ./source_me.sh && rm -Rf $(CWD)/$(INC_DIR)/bdsg && cd $(LIBBDSG_DIR) && $(MAKE) clean && CPLUS_INCLUDE_PATH=$(CWD)/$(INC_DIR):$(CWD)/$(INC_DIR)/dynamic:$(CPLUS_INCLUDE_PATH) CXXFLAGS="$(INCLUDE_FLAGS) -fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/libbdsg.a $(CWD)/$(LIB_DIR) && cp -r bdsg/include/* $(CWD)/$(INC_DIR)
+	+rm -Rf $(CWD)/$(INC_DIR)/bdsg && cd $(LIBBDSG_DIR) && $(MAKE) clean && CPLUS_INCLUDE_PATH=$(CWD)/$(INC_DIR):$(CWD)/$(INC_DIR)/dynamic:$(CPLUS_INCLUDE_PATH) CXXFLAGS="$(INCLUDE_FLAGS) -fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/libbdsg.a $(CWD)/$(LIB_DIR) && cp -r bdsg/include/* $(CWD)/$(INC_DIR)
 
 $(INC_DIR)/mio/mmap.hpp: $(MIO_DIR)/include/mio/*
-	+. ./source_me.sh && cp -r $(MIO_DIR)/include/mio $(CWD)/$(INC_DIR)/
+	+cp -r $(MIO_DIR)/include/mio $(CWD)/$(INC_DIR)/
 
 # It would be better to copy the atomic_queue directory rather than its contents, but to avoid re-writing mmmultimap...
 $(INC_DIR)/atomic_queue.h: $(ATOMIC_QUEUE_DIR)/include/*
-	+. ./source_me.sh && cp -r $(ATOMIC_QUEUE_DIR)/include/atomic_queue/* $(CWD)/$(INC_DIR)/
+	+cp -r $(ATOMIC_QUEUE_DIR)/include/atomic_queue/* $(CWD)/$(INC_DIR)/
 
 $(INC_DIR)/mmmultiset.hpp: $(MMMULTIMAP_DIR)/src/mmmultiset.hpp $(INC_DIR)/mmmultimap.hpp
 $(INC_DIR)/mmmultimap.hpp: $(MMMULTIMAP_DIR)/src/mmmultimap.hpp $(MMMULTIMAP_DIR)/src/mmmultiset.hpp $(INC_DIR)/mio/mmap.hpp $(INC_DIR)/atomic_queue.h
-	+. ./source_me.sh && cp $(MMMULTIMAP_DIR)/src/mmmultimap.hpp $(MMMULTIMAP_DIR)/src/mmmultiset.hpp $(CWD)/$(INC_DIR)/
+	+cp $(MMMULTIMAP_DIR)/src/mmmultimap.hpp $(MMMULTIMAP_DIR)/src/mmmultiset.hpp $(CWD)/$(INC_DIR)/
 
 $(INC_DIR)/ips4o.hpp: $(IPS4O_DIR)/ips4o.hpp $(IPS4O_DIR)/ips4o/*
-	+. ./source_me.sh && cp -r $(IPS4O_DIR)/ips4o* $(CWD)/$(INC_DIR)/
+	+cp -r $(IPS4O_DIR)/ips4o* $(CWD)/$(INC_DIR)/
 
 # The xg repo has a cmake build system based all around external projects, and
 # we need it to use our installed versions of everything instead.
@@ -860,7 +861,7 @@ $(INC_DIR)/ips4o.hpp: $(IPS4O_DIR)/ips4o.hpp $(IPS4O_DIR)/ips4o/*
 $(LIB_DIR)/libxg.a: $(XG_DIR)/src/*.hpp $(XG_DIR)/src/*.cpp $(INC_DIR)/mmmultimap.hpp $(INC_DIR)/ips4o.hpp $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(INC_DIR)/mio/mmap.hpp $(INC_DIR)/atomic_queue.h
 	+rm -f $@
 	+cp -r $(XG_DIR)/src/*.hpp $(CWD)/$(INC_DIR)
-	+. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -DNO_GFAKLUGE -c -o $(XG_DIR)/xg.o $(XG_DIR)/src/xg.cpp $(FILTER)
+	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -DNO_GFAKLUGE -c -o $(XG_DIR)/xg.o $(XG_DIR)/src/xg.cpp $(FILTER)
 	+ar rs $@ $(XG_DIR)/xg.o
 
 # Auto-git-versioning
@@ -922,42 +923,42 @@ $(OBJ_DIR)/version.o: $(SRC_DIR)/version.cpp $(SRC_DIR)/version.hpp $(SRC_DIR)/v
 # Use static pattern rules so the dependency files will not be ignored if the output exists
 # See <https://stackoverflow.com/a/34983297>
 $(OBJ) $(OBJ_DIR)/main.o: $(OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp $(OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(SHARED_OBJ): $(SHARED_OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp $(SHARED_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
 	@touch $@
 $(ALGORITHMS_OBJ): $(ALGORITHMS_OBJ_DIR)/%.o : $(ALGORITHMS_SRC_DIR)/%.cpp $(ALGORITHMS_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(ALGORITHMS_SHARED_OBJ): $(ALGORITHMS_SHARED_OBJ_DIR)/%.o : $(ALGORITHMS_SRC_DIR)/%.cpp $(ALGORITHMS_SHARED_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
 	@touch $@
 $(IO_OBJ): $(IO_OBJ_DIR)/%.o : $(IO_SRC_DIR)/%.cpp $(IO_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(IO_SHARED_OBJ): $(IO_SHARED_OBJ_DIR)/%.o : $(IO_SRC_DIR)/%.cpp $(IO_SHARED_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
 	@touch $@
 $(SUBCOMMAND_OBJ): $(SUBCOMMAND_OBJ_DIR)/%.o : $(SUBCOMMAND_SRC_DIR)/%.cpp $(SUBCOMMAND_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(UNITTEST_OBJ): $(UNITTEST_OBJ_DIR)/%.o : $(UNITTEST_SRC_DIR)/%.cpp $(UNITTEST_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(UNITTEST_SUPPORT_OBJ): $(UNITTEST_SUPPORT_OBJ_DIR)/%.o : $(UNITTEST_SUPPORT_SRC_DIR)/%.cpp $(UNITTEST_SUPPORT_OBJ_DIR)/%.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 	
 # Config objects get individual rules
 $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.d $(DEPS) $(LIB_DIR)/libjemalloc.a
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(CONFIG_OBJ_DIR)/allocator_config_jemalloc_debug.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc_debug.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc_debug.d $(DEPS) $(LIB_DIR)/libjemalloc_debug.a
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 $(CONFIG_OBJ_DIR)/allocator_config_system.o: $(CONFIG_SRC_DIR)/allocator_config_system.cpp $(CONFIG_OBJ_DIR)/allocator_config_system.d $(DEPS)
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+	$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
 	@touch $@
 
 # Use a fake rule to build .d files, so we don't complain if they don't exist.
diff --git a/README.md b/README.md
index 200ecff311c..b80954cadff 100644
--- a/README.md
+++ b/README.md
@@ -101,7 +101,7 @@ Note that a 64-bit OS is required. Ubuntu 20.04 should work.
 
 #### Linux: Build
 
-When you are ready, build with `. ./source_me.sh && make`. You can use `make -j16` to run 16 build threads at a time, which greatly accelerates the process. If you have more CPU cores, you can use higher numbers.
+When you are ready, build with `make`. You can use `make -j16` to run 16 build threads at a time, which greatly accelerates the process. If you have more CPU cores, you can use higher numbers.
 
 Note that vg can take anywhere from 10 minutes to more than an hour to compile depending on your machine and the number of threads used. 
 
@@ -161,7 +161,7 @@ Homebrew provides another package management solution for OSX, and may be prefer
 
 With dependencies installed, VG can now be built:
 
-    . ./source_me.sh && make
+    make
 
 As with Linux, you can add `-j16` or other numbers at the end to run multiple build tasks at once, if your computer can handle them.
     
diff --git a/configure.py b/configure.py
deleted file mode 100644
index 1290b07696d..00000000000
--- a/configure.py
+++ /dev/null
@@ -1,44 +0,0 @@
-import os
-import sys
-import shutil
-
-
-def make_source_me():
-    var_dict = {
-            "LIBRARY_PATH":"lib",
-            "LD_LIBRARY_PATH":"lib",
-            "LD_INCLUDE_PATH":"include",
-            "C_INCLUDE_PATH":"include",
-            "CPLUS_INCLUDE_PATH":"include",
-            "INCLUDE_PATH":"include",
-            "PATH":"bin"                                                                   }
-
-    my_wd = os.getcwd()
-    out_file = "source_me.sh"
-
-    with open(out_file, "w") as ofi:
-        for i in var_dict:
-            o_line  = "export" + " " + i + "=" + my_wd + "/" + var_dict[i] + ":$" + i + "\n"
-            ofi.write(o_line)
-
-def set_compiler():
-    compiler_dict = {
-        "CC": "gcc",
-        "CXX": "g++"
-        }
-
-    out_file = "source_me.sh"
-    with open(out_file, "a") as ofi:
-        for i in compiler_dict:
-            o_line = "export" + " " + i + "=" + "$(which " + compiler_dict[i] + ")\n"
-            ofi.write(o_line)
-
-def check_deps():
-    return
-
-## pulled these out with this line: for i in `cat source_me.sh | cut -f 2 -d " " | cut -f 1 -d "="`; do echo "\"\$$i\":\"\","; done
-if __name__ == "__main__":
-    make_source_me() 
-    set_compiler()
-## "$CC":"",
-            #"$CXX":"",  
diff --git a/deps/libbdsg b/deps/libbdsg
index 33e2fc213eb..e98cda26c25 160000
--- a/deps/libbdsg
+++ b/deps/libbdsg
@@ -1 +1 @@
-Subproject commit 33e2fc213eb492a0db38a30ecc1b3b4e3146e769
+Subproject commit e98cda26c2522bee80292705494dca8dcffa1c5c
diff --git a/deps/sdsl-lite b/deps/sdsl-lite
index 863d0118cf3..86fa3534c1b 160000
--- a/deps/sdsl-lite
+++ b/deps/sdsl-lite
@@ -1 +1 @@
-Subproject commit 863d0118cf303f9c9c55576e0f6b2f70ecd9689a
+Subproject commit 86fa3534c1bf02b5468bbe58e2e0b8f6ae2d6fa4
diff --git a/doc/wiki b/doc/wiki
index f70ea363837..f28a1e56005 160000
--- a/doc/wiki
+++ b/doc/wiki
@@ -1 +1 @@
-Subproject commit f70ea36383784fc731454c1b09014f65ad4f74d5
+Subproject commit f28a1e56005c729cf5c2dad6a251447bedba2949
diff --git a/scripts/setup-server b/scripts/setup-server
index e3965b61ca9..794f12d1917 100644
--- a/scripts/setup-server
+++ b/scripts/setup-server
@@ -36,7 +36,7 @@ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 100 --slave
 git clone --recursive https://github.com/vgteam/vg.git
 
 # build vg
-cd vg && source ./source_me.sh && make -j 32 static && sudo cp bin/vg /usr/local/bin/
+cd vg && make -j 32 static && sudo cp bin/vg /usr/local/bin/
 sudo cp scripts/vg_sim_pos_compare.py /usr/local/bin/
 cd ~
 
diff --git a/source_me.sh b/source_me.sh
old mode 100755
new mode 100644
index 0bb948c9280..d650cc14afe
--- a/source_me.sh
+++ b/source_me.sh
@@ -1,23 +1,4 @@
-export LIBRARY_PATH=`pwd`/lib:$LIBRARY_PATH
-export LD_LIBRARY_PATH=`pwd`/lib:$LD_LIBRARY_PATH
-export DYLD_LIBRARY_PATH=`pwd`/lib:$DYLD_LIBRARY_PATH
-export LD_INCLUDE_PATH=`pwd`/include:$LD_INCLUDE_PATH
-# Setting include directories via C_INCLUDE_PATH/CPLUS_INCLUDE_PATH will
-# automatically get them demoted to the end of the search list even if a -I
-# option is passed to try and bump them up earlier, before other -I options.
-# We leave the Makefile in charge of finding all the include directories.
-export CFLAGS="-I $(pwd)/include ${CFLAGS}"
-export CXXFLAGS="-I $(pwd)/include -I$(pwd)/include/dynamic ${CXXFLAGS}"
-export PATH=`pwd`/bin:`pwd`/scripts:"$PATH"
-export CC=$(which gcc)
-export CXX=$(which g++)
-
-#
-#  disable until file arguments work as in normal bash :(
-#
-# add bash autocompletion
-#if test -n "$BASH_VERSION"
-#then
-#
-#	 . ./autocomp.bash
-#fi
+# We used to have a script here to set up all the include and library search
+# paths for the vg build. But now the Makefile knows how to do it all for the
+# build, and the vg binary knows where to look for its dynamic libraries.
+echo 1>&2 "Sourcing source_me.sh is no longer necessary"
diff --git a/src/deconstructor.cpp b/src/deconstructor.cpp
index aa052db955a..0f15b8139d7 100644
--- a/src/deconstructor.cpp
+++ b/src/deconstructor.cpp
@@ -1168,9 +1168,10 @@ string Deconstructor::get_vcf_header() {
     }
 
     if (sample_to_haps.empty()) {
-        cerr << "Error [vg deconstruct]: No paths found for alt alleles in the graph. Note that "
-             << "exhaustive path-free traversal finding is no longer supported, and vg deconstruct "
-             << "now only works on embedded paths and GBWT threads." << endl;
+        cerr << "Error [vg deconstruct]: No paths other than selected reference(s) found in the graph, "
+             << "so no alt alleles can be generated. Note that exhaustive path-free traversal finding "
+             << "is no longer supported, and vg deconstruct now only works on embedded paths and GBWT "
+             << "threads." << endl;
         exit(1);
     }
 
diff --git a/src/subcommand/chunk_main.cpp b/src/subcommand/chunk_main.cpp
index 22f6e02651e..57397ed6713 100644
--- a/src/subcommand/chunk_main.cpp
+++ b/src/subcommand/chunk_main.cpp
@@ -349,6 +349,36 @@ int main_chunk(int argc, char** argv) {
     bool chunk_gam = !gam_files.empty() && gam_split_size == 0;
     bool chunk_graph = gam_and_graph || (!chunk_gam && gam_split_size == 0);
 
+    // parse the regions into a list before loading the graph, if we're
+    // specifying regions by path name.
+    vector<Region> regions;
+    if (!region_strings.empty()) {
+        for (auto& region_string : region_strings) {
+            Region region;
+            parse_region(region_string, region);
+            regions.push_back(region);
+        }
+    }
+    if (!path_list_file.empty()) {
+        ifstream pr_stream(path_list_file.c_str());
+        if (!pr_stream) {
+            cerr << "error:[vg chunk] unable to open path regions: " << path_list_file << endl;
+            return 1;
+        }
+        while (pr_stream) {
+            string buf;
+            std::getline(pr_stream, buf);
+            if (!buf.empty()) {
+                Region region;
+                parse_region(buf, region);
+                regions.push_back(region);
+            }
+        }
+    }
+    if (!in_bed_file.empty()) {
+        parse_bed_regions(in_bed_file, regions);
+    }
+
     // Load the snarls
     unique_ptr<SnarlManager> snarl_manager;
     if (!snarl_filename.empty()) {
@@ -377,9 +407,17 @@ int main_chunk(int argc, char** argv) {
             return 1;
         }
         in.close();
+
+        // To support the regions we were asked for, we might need to ensure
+        // the paths they are on are actually indexed for reference style
+        // offset lookups.
+        std::unordered_set<std::string> ensure_indexed;
+        for (auto& region : regions) {
+            ensure_indexed.insert(region.seq);
+        }
         
         path_handle_graph = vg::io::VPKG::load_one<PathHandleGraph>(xg_file);
-        graph = overlay_helper.apply(path_handle_graph.get());
+        graph = overlay_helper.apply(path_handle_graph.get(), ensure_indexed);
         in.close();
     }
 
@@ -463,35 +501,7 @@ int main_chunk(int argc, char** argv) {
     // (instead of an index)
     unordered_map<nid_t, int32_t> node_to_component;
     
-    // parse the regions into a list
-    vector<Region> regions;
-    if (!region_strings.empty()) {
-        for (auto& region_string : region_strings) {
-            Region region;
-            parse_region(region_string, region);
-            regions.push_back(region);
-        }
-    }
-    else if (!path_list_file.empty()) {
-        ifstream pr_stream(path_list_file.c_str());
-        if (!pr_stream) {
-            cerr << "error:[vg chunk] unable to open path regions: " << path_list_file << endl;
-            return 1;
-        }
-        while (pr_stream) {
-            string buf;
-            std::getline(pr_stream, buf);
-            if (!buf.empty()) {
-                Region region;
-                parse_region(buf, region);
-                regions.push_back(region);
-            }
-        }
-    }
-    else if (!in_bed_file.empty()) {
-        parse_bed_regions(in_bed_file, regions);
-    }
-    else if (id_range) {
+    if (id_range) {
         if (n_chunks) {
             // Determine the ranges from the source graph itself.
             // how many nodes per range?
@@ -556,9 +566,9 @@ int main_chunk(int argc, char** argv) {
             delete range_stream;
         }
     }
-    else if (graph != nullptr && (!components || path_components)) {
-        // every path
-        graph->for_each_path_handle([&](path_handle_t path_handle) {
+    if (graph != nullptr && path_components) {
+        // every reference or generic path (guaranteed to be reference indexed)
+        graph->for_each_path_matching({PathSense::REFERENCE, PathSense::GENERIC}, {}, {}, [&](path_handle_t path_handle) {
                 Region region;
                 region.seq = graph->get_path_name(path_handle);
                 if (!Paths::is_alt(region.seq)) {
@@ -596,7 +606,7 @@ int main_chunk(int argc, char** argv) {
     if (!id_range) {
         for (auto& region : regions) {
             if (!graph->has_path(region.seq)) {
-                cerr << "error[vg chunk]: input path " << region.seq << " not found in xg index" << endl;
+                cerr << "error[vg chunk]: input path " << region.seq << " not found in graph" << endl;
                 return 1;
             }
             region.start = max((int64_t)0, region.start);
diff --git a/src/subcommand/paths_main.cpp b/src/subcommand/paths_main.cpp
index fb668d7edd4..cda4be4256b 100644
--- a/src/subcommand/paths_main.cpp
+++ b/src/subcommand/paths_main.cpp
@@ -18,6 +18,7 @@
 #include "../gbwt_helper.hpp"
 #include "../traversal_clusters.hpp"
 #include "../io/save_handle_graph.hpp"
+#include <bdsg/overlays/overlay_helper.hpp>
 #include <vg/io/vpkg.hpp>
 #include <vg/io/stream.hpp>
 #include <vg/io/alignment_emitter.hpp>
@@ -57,6 +58,8 @@ void help_paths(char** argv) {
          << "    -G, --generic-paths      select the generic, non-reference, non-haplotype paths" << endl
          << "    -R, --reference-paths    select the reference paths" << endl
          << "    -H, --haplotype-paths    select the haplotype paths paths" << endl
+         << "  configuration:" << endl
+         << "    -o, --overlay            apply a ReferencePathOverlayHelper to the graph" << endl
          << "    -t, --threads N          number of threads to use [all available]. applies only to snarl finding within -n" << endl;
 }
 
@@ -122,6 +125,7 @@ int main_paths(int argc, char** argv) {
     bool coverage = false;
     const size_t coverage_bins = 10;
     bool normalize_paths = false;
+    bool overlay = false;
 
     int c;
     optind = 2; // force optind past command positional argument
@@ -151,6 +155,7 @@ int main_paths(int argc, char** argv) {
             {"reference-paths", no_argument, 0, 'R'},
             {"haplotype-paths", no_argument, 0, 'H'},
             {"coverage", no_argument, 0, 'c'},            
+            {"overlay", no_argument, 0, 'o'},
 
             // Hidden options for backward compatibility.
             {"threads", no_argument, 0, 'T'},
@@ -160,7 +165,7 @@ int main_paths(int argc, char** argv) {
         };
 
         int option_index = 0;
-        c = getopt_long (argc, argv, "hLXv:x:g:Q:VEMCFAS:Tq:drnaGRHp:ct:",
+        c = getopt_long (argc, argv, "hLXv:x:g:Q:VEMCFAS:drnaGRHp:coTq:t:",
                 long_options, &option_index);
 
         // Detect the end of the options.
@@ -276,6 +281,10 @@ int main_paths(int argc, char** argv) {
             output_formats++;
             break;
 
+        case 'o':
+            overlay = true;
+            break;
+
         case 'T':
             std::cerr << "warning: [vg paths] option --threads is obsolete and unnecessary" << std::endl;
             break;
@@ -375,11 +384,23 @@ int main_paths(int argc, char** argv) {
     
     // Load whatever indexes we were given
     // Note: during handlifiction, distinction between -v and -x options disappeared.
-    unique_ptr<PathHandleGraph> graph;
+    unique_ptr<PathHandleGraph> path_handle_graph;
     if (!graph_file.empty()) {
         // Load the graph
-        graph = vg::io::VPKG::load_one<PathHandleGraph>(graph_file);
+        path_handle_graph = vg::io::VPKG::load_one<PathHandleGraph>(graph_file);
+    }
+    bdsg::ReferencePathOverlayHelper overlay_helper;
+    PathHandleGraph* graph = nullptr;
+    if (path_handle_graph) {
+        if (overlay) {
+            // Try to apply the overlay if the user wanted it and this isn't
+            // already a graph implementing position lookups.
+            graph = overlay_helper.apply(path_handle_graph.get());
+        } else {
+            graph = path_handle_graph.get();
+        }
     }
+
     unique_ptr<gbwt::GBWT> gbwt_index;
     if (!gbwt_file.empty()) {
         // We want a gbwt
@@ -418,7 +439,7 @@ int main_paths(int argc, char** argv) {
     if (extract_as_gam || extract_as_gaf) {
         // Open up a GAM/GAF output stream
         aln_emitter = vg::io::get_non_hts_alignment_emitter("-", extract_as_gaf ? "GAF" : "GAM", {}, get_thread_count(),
-                                                            graph.get());
+                                                            graph);
     } else if (extract_as_vg) {
         // Open up a VG Graph chunk output stream
         graph_emitter = unique_ptr<vg::io::ProtobufEmitter<Graph>>(new vg::io::ProtobufEmitter<Graph>(cout));
@@ -589,7 +610,7 @@ int main_paths(int argc, char** argv) {
         };
         
         if (drop_paths || retain_paths || normalize_paths) {
-            MutablePathMutableHandleGraph* mutable_graph = dynamic_cast<MutablePathMutableHandleGraph*>(graph.get());
+            MutablePathMutableHandleGraph* mutable_graph = dynamic_cast<MutablePathMutableHandleGraph*>(graph);
             if (!mutable_graph) {
                 std::cerr << "error[vg paths]: graph cannot be modified" << std::endl;
                 exit(1);
diff --git a/test/Makefile b/test/Makefile
index 5ae913873f1..bdf0526ace7 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -20,7 +20,7 @@ $(vg):
 	cd .. && $(MAKE) bin/vg
 
 build_graph: build_graph.cpp
-	cd .. && . ./source_me.sh && $(MAKE) test/build_graph
+	cd .. && $(MAKE) test/build_graph
 
 clean:
 	rm -f build_graph
diff --git a/test/t/30_vg_chunk.t b/test/t/30_vg_chunk.t
index 20c8466ea88..142de98066a 100644
--- a/test/t/30_vg_chunk.t
+++ b/test/t/30_vg_chunk.t
@@ -5,7 +5,7 @@ BASH_TAP_ROOT=../deps/bash-tap
 
 PATH=../bin:$PATH # for vg
 
-plan tests 32
+plan tests 35
 
 # Construct a graph with alt paths so we can make a GBWT and a GBZ
 vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz -a >x.vg
@@ -126,5 +126,15 @@ is "$?" 0 "components finds subgraphs"
 
 rm -f xy.vg x.vg y.vg x_nodes.txt y_nodes.txt convert path_chunk_x.vg  convert path_chunk_y.vg pc_x_nodes.txt pc_y_nodes.txt x_paths.txt pc_x_paths.txt components_chunk_0.vg components_chunk_1.vg comp_0_nodes.txt comp_1_nodes.txt comp_nodes.txt nodes.txt x.gam y.gam xy.gam path_chunk_x.gam path_chunk_y.gam
 
+vg gbwt --gbz-format --graph-name graph.gbz --gfa-input graphs/gfa_with_reference.gfa
+vg chunk -x graph.gbz -p sample1#1#chr1#0:1-2 -c 1 >part.vg 2>log.txt
+grep "out_of_range" log.txt
+is "$?" "1" "chunking on a haplotype path does not produce an out of range error"
+grep "not found in" log.txt
+is "$?" "1" "chunking on a haplotype path does not produce a path not found error"
+is "$(vg stats -z part.vg | grep nodes | cut -f2)" "4" "chunking on a haplotype produces the correct size graph"
+
+rm -f graph.gbz part.vg log.txt
+
 
 
diff --git a/vgci/vgci.sh b/vgci/vgci.sh
index 4526dac20aa..9a5e53b08f3 100755
--- a/vgci/vgci.sh
+++ b/vgci/vgci.sh
@@ -252,7 +252,6 @@ then
     if [ "${LOCAL_BUILD}" == "1" ]
     then
         # Just build vg here
-        . ./source_me.sh
         make -j ${NUM_CORES}
 
         if [ "$?" -ne 0 ]