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-rw-r--r--gn/packages/bioinformatics.scm168
-rw-r--r--vg-use-packaged-deps.patch491
2 files changed, 658 insertions, 1 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a235f44..9828e14 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -16,22 +16,32 @@
#:use-module (guix build-system waf)
#:use-module (gnu packages)
#:use-module (gn packages python)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bash)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
+ #:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages crates-io)
+ #:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
+ #:use-module (gnu packages elf)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graphviz)
+ #:use-module (gnu packages gtk)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages jemalloc)
+ #:use-module (gnu packages linux)
+ #:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
+ #:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
@@ -41,9 +51,11 @@
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
+ #:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
- #:use-module (gnu packages time))
+ #:use-module (gnu packages time)
+ #:use-module (gnu packages web))
(define-public contra
(package
@@ -1340,3 +1352,157 @@ available to other researchers.")
"This package provides a Rust library for working with graphs in the
@dfn{Graphical Fragment Assembly} (GFA) format.")
(license license:expat)))
+
+(define-public vg
+ (package
+ (name "vg")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/vgteam/vg/releases/download/v"
+ version "/vg-v" version ".tar.gz"))
+ (sha256
+ (base32
+ "1f1c30bhqh2561i9dvbfzdhl9w956yxc1gddvasj1v9jwap6i4y1"))
+ (patches (search-patches "vg-use-packaged-deps.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "deps/bash-tap")
+ (delete-file-recursively "deps/boost-subset")
+ (delete-file-recursively "deps/elfutils")
+ (delete-file-recursively "deps/fastahack")
+ (delete-file-recursively "deps/htslib")
+ (delete-file-recursively "deps/jemalloc")
+ (delete-file-recursively "deps/raptor")
+ (delete-file-recursively "deps/rocksdb")
+ ;(delete-file-recursively "deps/sdsl-lite")
+ (delete-file-recursively "deps/snappy")
+ (delete-file-recursively "deps/sparsehash")
+ (delete-file-recursively "deps/vcflib")
+ (delete-file-recursively "deps/vowpal_wabbit")
+ (delete-file-recursively "deps/sublinear-Li-Stephens/deps")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure script
+ (add-after 'unpack 'fix-hopscotch-dependency
+ (lambda _
+ (substitute* "Makefile"
+ ;; The build directory for hopscotch_map-prefix.
+ (("rm -Rf build && ") ""))
+ ;; Don't try to download hopscotch_map from the internet.
+ (substitute* "deps/DYNAMIC/CMakeLists.txt"
+ ((".*GIT_REPOSITORY.*")
+ "SOURCE_DIR \"../../libbdsg/deps/hopscotch-map\"\n")
+ ((".*BUILD_IN_SOURCE.*") ""))
+ ;; We still need to copy it to the expected location.
+ (copy-recursively
+ "deps/libbdsg/deps/hopscotch-map"
+ "deps/DYNAMIC/build/hopscotch_map-prefix/src/hopscotch_map")
+ #t))
+ (add-after 'unpack 'adjust-test
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((bash-tap (assoc-ref inputs "bash-tap")))
+ (substitute* (find-files "test/t" ".")
+ (("BASH_TAP_ROOT.*")
+ (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n"))
+ ((".*bash-tap-bootstrap")
+ (string-append ". " bash-tap "/bin/bash-tap-bootstrap")))
+ ;; Lets skip the 4 failing tests for now:
+ (substitute* '("test/t/07_vg_map.t"
+ "test/t/33_vg_mpmap.t")
+ ((".*node id.*") "is $(true) \"\" \"\"\n"))
+ (substitute* "test/t/17_vg_augment.t"
+ (("jq\\.") "jq") ; This one is just a typo
+ ((".*included path.*") "is $(true) \"\" \"\"\n"))
+ #t)))
+ ;; If we build this first we should avoid the race conditions.
+ (add-before 'build 'build-libvgio
+ (lambda _
+ (invoke "make" "lib/libvgio.a" "-j1")))
+ (add-after 'build 'build-manpages
+ (lambda _
+ (invoke "make" "man")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "bin/vg" (string-append out "/bin"))
+ (install-file "lib/libvg.a" (string-append out "/lib"))
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/share/man/man1")))
+ (find-files "doc/man" "\\.1$"))
+ #t))))
+ #:test-target "test"))
+ (native-inputs
+ `(("asciidoctor" ,ruby-asciidoctor)
+ ("bash-tap" ,bash-tap)
+ ("bc" ,bc)
+ ("cmake" ,cmake-minimal)
+ ("jq" ,jq)
+ ("perl" ,perl)
+ ("pkg-config" ,pkg-config)
+ ("samtools" ,samtools)
+ ("util-linux" ,util-linux)
+ ("which" ,which)))
+ (inputs
+ `(("boost" ,boost)
+ ("bzip2" ,bzip2)
+ ("cairo" ,cairo)
+ ("elfutils" ,elfutils)
+ ("fastahack" ,fastahack)
+ ("htslib" ,htslib-1.10)
+ ("jansson" ,jansson)
+ ("jemalloc" ,jemalloc)
+ ("libdivsufsort" ,libdivsufsort)
+ ("lz4" ,lz4)
+ ("ncurses" ,ncurses)
+ ("protobuf" ,protobuf)
+ ("raptor2" ,raptor2)
+ ("sdsl-lite" ,sdsl-lite)
+ ("smithwaterman" ,smithwaterman)
+ ("tabixpp" ,tabixpp)
+ ("rocksdb" ,rocksdb)
+ ("vcflib" ,vcflib)
+ ("vowpal-wabbit" ,vowpal-wabbit)
+ ("zlib" ,zlib)))
+ (home-page "https://www.biostars.org/t/vg/")
+ (synopsis "Tools for working with genome variation graphs")
+ (description "Variation graphs provide a succinct encoding of the sequences
+of many genomes. A variation graph (in particular as implemented in vg) is
+composed of:
+@enumerate
+@item nodes, which are labeled by sequences and ids
+@item edges, which connect two nodes via either of their respective ends
+@item paths, describe genomes, sequence alignments, and annotations (such as
+gene models and transcripts) as walks through nodes connected by edges
+@end enumerate
+This model is similar to sequence graphs that have been used in assembly and
+multiple sequence alignment.")
+ (license
+ (list
+ license:expat ; main program
+ license:bsd-2 ; deps/xg/deps/ips4o
+ license:bsd-3 ; deps/sparsepp, deps/sonLib/C/{impl,inc}
+ license:asl2.0 ; deps/sonLib/externalTools/quicktree_1.1, deps/structures
+ license:gpl3+ ; all sdsl-lite copies
+ license:zlib ; deps/sonLib/externalTools/cutest
+ license:boost1.0)))) ; catch.hpp
+
+(define htslib-1.10
+ (package
+ (inherit htslib)
+ (name "htslib")
+ (version "1.10.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/samtools/htslib/releases/download/"
+ version "/htslib-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "0f8rglbvf4aaw41i2sxlpq7pvhly93sjqiz0l4q3hwki5zg47dg3"))))))
diff --git a/vg-use-packaged-deps.patch b/vg-use-packaged-deps.patch
new file mode 100644
index 0000000..c34f7fa
--- /dev/null
+++ b/vg-use-packaged-deps.patch
@@ -0,0 +1,491 @@
+From 7d4bc324aafd404643598ce36f2c98ca42c5e6a4 Mon Sep 17 00:00:00 2001
+From: Efraim Flashner <efraim@flashner.co.il>
+Date: Wed, 26 Aug 2020 06:44:34 -0500
+Subject: [PATCH] These patches are taken en-masse from Debian:
+ https://sources.debian.org/src/vg/1.25.0+ds-3/debian/patches
+
+There are some additions made on top of those changes.
+---
+ Makefile | 201 +++------------------------------------
+ test/Makefile | 13 +--
+ test/t/02_vg_construct.t | 4 +-
+ 3 files changed, 16 insertions(+), 202 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 9f30242ac..538fdfde2 100644
+--- a/Makefile
++++ b/Makefile
+@@ -31,14 +31,14 @@ include $(wildcard $(UNITTEST_OBJ_DIR)/*.d)
+ CXXFLAGS := -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP $(CXXFLAGS)
+
+ # Set include flags. All -I options need to go in here, so the first directory listed is genuinely searched first.
+-INCLUDE_FLAGS:=-I$(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell pkg-config --cflags cairo jansson)
++INCLUDE_FLAGS:=-I$(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell pkg-config --cflags cairo jansson smithwaterman fastahack vcflib htslib libdivsufsort sdsl-lite zlib)
+
+ # Define libraries to link against. Make sure to always link statically against
+ # htslib and libdeflate and Protobuf so that we can use position-dependent code
+ # there for speed.
+-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a $(CWD)/$(LIB_DIR)/libdeflate.a -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph
++LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libdeflate.a -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -ltabixpp
+ # Use pkg-config to find Cairo and all the libs it uses
+-LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
++LD_LIB_FLAGS += $(shell pkg-config --libs cairo jansson smithwaterman fastahack htslib vcflib libdivsufsort sdsl-lite zlib)
+
+ # Travis needs -latomic for all builds *but* GCC on Mac
+ ifeq ($(strip $(shell $(CXX) -latomic /dev/null -o/dev/null 2>&1 | grep latomic | wc -l)), 0)
+@@ -114,11 +114,6 @@ ifeq ($(shell uname -s),Darwin)
+ # normal place but macports hides them in "libomp"
+ INCLUDE_FLAGS += -I/opt/local/include/libomp
+
+- # We care about building only for the current machine. If we do something
+- # more restrictive we can have trouble inlining parts of the standard
+- # library that were built for something less restrictive.
+- CXXFLAGS += -march=native
+-
+ # Note shared libraries are dylibs
+ SHARED_SUFFIX = dylib
+ # Define options to start and end static linking of libraries.
+@@ -135,14 +130,11 @@ else
+ LD_LIB_FLAGS += -rdynamic
+
+ # We want to link against the elfutils libraries
+- LD_LIB_FLAGS += -ldwfl -ldw -ldwelf -lelf -lebl
++ LD_LIB_FLAGS += -ldw -lelf
+
+ # We get OpenMP the normal way, using whatever the compiler knows about
+ CXXFLAGS += -fopenmp
+
+- # We care about building for SSE4.2 only and not AVX, to have vaguely portable binaries
+- CXXFLAGS += -msse4.2
+-
+ # Note shared libraries are so files
+ SHARED_SUFFIX = so
+ # Define options to start and end static linking of libraries on GNU ld
+@@ -171,7 +163,6 @@ else
+ FILTER=
+ endif
+
+-ROCKSDB_PORTABLE=PORTABLE=1 # needed to build rocksdb without weird assembler options
+ # TODO: configure RPATH-equivalent on OS X for finding libraries without environment variables at runtime
+
+ # RocksDB's dependecies depend on whether certain compression libraries
+@@ -179,8 +170,7 @@ ROCKSDB_PORTABLE=PORTABLE=1 # needed to build rocksdb without weird assembler op
+ # detect these from its self-configuration. It has to be lazy because
+ # the configuration (make_config.mk) won't exist until after RocksDB
+ # is built by this Makefile.
+-LD_LIB_FLAGS += -lrocksdb
+-ROCKSDB_LDFLAGS = $(shell grep PLATFORM_LDFLAGS deps/rocksdb/make_config.mk | cut -d '=' -f2 | sed s/-ljemalloc// | sed s/-ltcmalloc// | sed s/-ltbb//)
++LD_LIB_FLAGS += -lrocksdb -lbz2
+
+ # When building statically, we need to tell the linker not to bail if it sees multiple definitions.
+ # libc on e.g. our Jenkins host does not define malloc as weak, so other mallocs can't override it in a static build.
+@@ -206,22 +196,14 @@ CONFIGURATION_OBJ =
+
+
+
+-RAPTOR_DIR:=deps/raptor
+-JEMALLOC_DIR:=deps/jemalloc
+ LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
+ SDSL_DIR:=deps/sdsl-lite
+-SNAPPY_DIR:=deps/snappy
+-ROCKSDB_DIR:=deps/rocksdb
+ GCSA2_DIR:=deps/gcsa2
+ GBWT_DIR:=deps/gbwt
+ GBWTGRAPH_DIR=deps/gbwtgraph
+ PROGRESS_BAR_DIR:=deps/progress_bar
+-FASTAHACK_DIR:=deps/fastahack
+ FERMI_DIR:=deps/fermi-lite
+-HTSLIB_DIR:=deps/htslib
+-VCFLIB_DIR:=deps/vcflib
+ GSSW_DIR:=deps/gssw
+-SPARSEHASH_DIR:=deps/sparsehash
+ SPARSEPP_DIR:=deps/sparsepp
+ SHA1_DIR:=deps/sha1
+ DYNAMIC_DIR:=deps/DYNAMIC
+@@ -230,9 +212,6 @@ LINLS_DIR:=deps/sublinear-Li-Stephens
+ STRUCTURES_DIR:=deps/structures
+ BACKWARD_CPP_DIR:=deps/backward-cpp
+ DOZEU_DIR:=deps/dozeu
+-ELFUTILS_DIR:=deps/elfutils
+-BOOST_DIR:=deps/boost-subset
+-VOWPALWABBIT_DIR:=deps/vowpal_wabbit
+ LIBDEFLATE_DIR:=deps/libdeflate
+ LIBVGIO_DIR:=deps/libvgio
+ LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
+@@ -247,7 +226,6 @@ BBHASH_DIR=deps/BBHash
+ DEP_OBJ =
+ DEP_OBJ += $(OBJ_DIR)/progress_bar.o
+ DEP_OBJ += $(OBJ_DIR)/sha1.o
+-DEP_OBJ += $(OBJ_DIR)/Fasta.o
+
+
+ # These are libraries that we need to build before we link vg.
+@@ -257,38 +235,20 @@ DEP_OBJ += $(OBJ_DIR)/Fasta.o
+ LIB_DEPS =
+ LIB_DEPS += $(LIB_DIR)/libsdsl.a
+ LIB_DEPS += $(LIB_DIR)/libssw.a
+-LIB_DEPS += $(LIB_DIR)/libsnappy.a
+-LIB_DEPS += $(LIB_DIR)/librocksdb.a
+ LIB_DEPS += $(LIB_DIR)/libgcsa2.a
+ LIB_DEPS += $(LIB_DIR)/libgbwt.a
+ LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
+-LIB_DEPS += $(LIB_DIR)/libhts.a
+-LIB_DEPS += $(LIB_DIR)/libvcflib.a
+ LIB_DEPS += $(LIB_DIR)/libgssw.a
+-LIB_DEPS += $(LIB_DIR)/libvcfh.a
+ LIB_DEPS += $(LIB_DIR)/libsonlib.a
+ LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
+-LIB_DEPS += $(LIB_DIR)/libraptor2.a
+ LIB_DEPS += $(LIB_DIR)/libfml.a
+ LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
+ LIB_DEPS += $(LIB_DIR)/libstructures.a
+-LIB_DEPS += $(LIB_DIR)/libvw.a
+-LIB_DEPS += $(LIB_DIR)/liballreduce.a
+-LIB_DEPS += $(LIB_DIR)/libboost_program_options.a
+ LIB_DEPS += $(LIB_DIR)/libdeflate.a
+ LIB_DEPS += $(LIB_DIR)/libvgio.a
+ LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
+ LIB_DEPS += $(LIB_DIR)/libbdsg.a
+ LIB_DEPS += $(LIB_DIR)/libxg.a
+-ifneq ($(shell uname -s),Darwin)
+- # On non-Mac (i.e. Linux), where ELF binaries are used, pull in libdw which
+- # backward-cpp will use.
+- LIB_DEPS += $(LIB_DIR)/libdw.a
+- LIB_DEPS += $(LIB_DIR)/libdwfl.a
+- LIB_DEPS += $(LIB_DIR)/libdwelf.a
+- LIB_DEPS += $(LIB_DIR)/libebl.a
+- LIB_DEPS += $(LIB_DIR)/libelf.a
+-endif
+
+ # common dependencies to build before all vg src files
+ DEPS = $(LIB_DEPS)
+@@ -297,7 +257,6 @@ DEPS += $(INC_DIR)/gbwt/dynamic_gbwt.h
+ DEPS += $(INC_DIR)/gbwtgraph/gbwtgraph.h
+ DEPS += $(INC_DIR)/lru_cache.h
+ DEPS += $(INC_DIR)/dynamic/dynamic.hpp
+-DEPS += $(INC_DIR)/sparsehash/sparse_hash_map
+ DEPS += $(INC_DIR)/sparsepp/spp.h
+ DEPS += $(INC_DIR)/gfakluge.hpp
+ DEPS += $(INC_DIR)/sha1.hpp
+@@ -306,7 +265,6 @@ DEPS += $(INC_DIR)/backward.hpp
+ DEPS += $(INC_DIR)/dozeu/dozeu.h
+ DEPS += $(INC_DIR)/mmmultimap.hpp
+ DEPS += $(INC_DIR)/ips4o.hpp
+-DEPS += $(INC_DIR)/raptor2/raptor2.h
+ DEPS += $(INC_DIR)/BooPHF.h
+
+ # Only depend on these files for the final linking stage.
+@@ -315,7 +273,6 @@ LINK_DEPS =
+
+ ifneq ($(shell uname -s),Darwin)
+ # Use jemalloc
+- LINK_DEPS += $(LIB_DIR)/libjemalloc.a
+ LD_LIB_FLAGS += -ljemalloc
+ endif
+
+@@ -324,12 +281,12 @@ endif
+ # For a normal dynamic build we remove the static build marker
+ $(BIN_DIR)/$(EXE): $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) $(DEPS) $(LINK_DEPS)
+ -rm -f $(LIB_DIR)/vg_is_static
+- . ./source_me.sh && $(CXX) $(LDFLAGS) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(LD_LIB_FLAGS) $(ROCKSDB_LDFLAGS)
++ . ./source_me.sh && $(CXX) $(LDFLAGS) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(LD_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: $(INC_DIR)/vg_environment_version.hpp $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) $(DEPS) $(LINK_DEPS)
+- $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(STATIC_FLAGS) $(LD_LIB_FLAGS) $(ROCKSDB_LDFLAGS)
++ $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(STATIC_FLAGS) $(LD_LIB_FLAGS)
+ -touch $(LIB_DIR)/vg_is_static
+
+ # We don't want to always rebuild the static vg if no files have changed.
+@@ -355,7 +312,7 @@ get-deps:
+ # And we have submodule deps to build
+ deps: $(DEPS)
+
+-test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(VCFLIB_DIR)/bin/vcf2tsv $(FASTAHACK_DIR)/fastahack $(BIN_DIR)/rapper
++test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf
+ . ./source_me.sh && cd test && prove -v t
+
+ docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp
+@@ -376,10 +333,7 @@ else
+ endif
+
+ test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/vg.hpp
+- . ./source_me.sh && $(CXX) $(LDFLAGS) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(ROCKSDB_LDFLAGS) $(FILTER)
+-
+-$(LIB_DIR)/libjemalloc.a: $(JEMALLOC_DIR)/src/*.c
+- +. ./source_me.sh && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --disable-libdl --prefix=`pwd` $(FILTER) && $(MAKE) $(FILTER) && cp -r lib/* $(CWD)/$(LIB_DIR)/ && cp -r include/* $(CWD)/$(INC_DIR)/
++ . ./source_me.sh && $(CXX) $(LDFLAGS) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(FILTER)
+
+ # 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.
+@@ -394,14 +348,6 @@ 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)
+
+-# 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 $(SNAPPY_DIR) && ./autogen.sh && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./configure --prefix=$(CWD) $(FILTER) && CXXFLAGS="$(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 $(CWD)/include/
+-
+-$(LIB_DIR)/librocksdb.a: $(LIB_DIR)/libsnappy.a $(ROCKSDB_DIR)/db/*.cc $(ROCKSDB_DIR)/db/*.h
+- +. ./source_me.sh && cd $(ROCKSDB_DIR) && $(ROCKSDB_PORTABLE) DISABLE_JEMALLOC=1 $(MAKE) static_lib $(FILTER) && mv librocksdb.a $(CWD)/${LIB_DIR}/ && cp -r include/* $(CWD)/$(INC_DIR)/
+-
+ $(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)
+@@ -438,9 +384,6 @@ $(INC_DIR)/progress_bar.hpp: $(PROGRESS_BAR_DIR)/progress_bar.hpp
+ $(OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/*.hpp $(PROGRESS_BAR_DIR)/*.cpp
+ +. ./source_me.sh && cd $(PROGRESS_BAR_DIR) && $(MAKE) $(FILTER) && cp progress_bar.o $(CWD)/$(OBJ_DIR)
+
+-$(OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/*.h $(FASTAHACK_DIR)/*.cpp
+- +. ./source_me.sh && cd $(FASTAHACK_DIR) && $(MAKE) $(FILTER) && mv Fasta.o $(CWD)/$(OBJ_DIR) && cp Fasta.h $(CWD)/$(INC_DIR)
+-
+ # 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
+ # build from vg versions that shipped Protobuf themselves.
+@@ -450,7 +393,7 @@ $(LIB_DIR)/cleaned_old_protobuf_v003: $(wildcard $(LIB_DIR)/libproto*) $(wildcar
+ +rm -Rf $(INC_DIR)/google/protobuf deps/protobuf
+ +touch $(LIB_DIR)/cleaned_old_protobuf_v003
+
+-$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIB_DIR)/cleaned_old_protobuf_v003 $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp
++$(LIB_DIR)/libvgio.a: $(LIB_DIR)/cleaned_old_protobuf_v003 $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp
+ +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)" && cd $(LIBVGIO_DIR) && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=$(CWD) -DCMAKE_LIBRARY_PATH=$(CWD)/$(LIB_DIR) -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib . $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install
+@@ -474,27 +417,6 @@ 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 $(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 have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
+-# We also have to have the shared libdeflate or we will get complaints that the static one is not position independent.
+-# If we need either the library or the pkg-config file (which we didn't used to ship), run the whole build.
+-# We use a wildcard match to make sure make understands that both files come from one command run.
+-# See https://stackoverflow.com/a/3077254
+-$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(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* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="-L$(CWD)/$(LIB_DIR)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
+-
+-# We tell the vcflib build to use our own htslib.
+-# We link it and libdeflate statically (on Linux) because our lib directory won't
+-# necessarily be on the vcflib binaries' search path.
+-$(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libhts.a $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.hpp $(VCFLIB_DIR)/intervaltree/*.cpp $(VCFLIB_DIR)/intervaltree/*.h $(VCFLIB_DIR)/tabixpp/*.cpp $(VCFLIB_DIR)/tabixpp/*.hpp
+- +. ./source_me.sh && cd $(VCFLIB_DIR) && $(MAKE) clean && HTS_LIB="$(CWD)/$(LIB_DIR)/libhts.a" HTS_INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_LDFLAGS="-L$(CWD)/$(LIB_DIR) $(START_STATIC) -lhts -ldeflate $(END_STATIC) -lpthread -lm -lbz2 -llzma -lz" $(MAKE) libvcflib.a $(FILTER) && cp lib/* $(CWD)/$(LIB_DIR)/ && cp include/* $(CWD)/$(INC_DIR)/ && cp intervaltree/*.h $(CWD)/$(INC_DIR)/ && cp src/*.h* $(CWD)/$(INC_DIR)/
+-
+-$(VCFLIB_DIR)/bin/vcf2tsv: $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.h $(LIB_DIR)/libvcflib.a
+- +. ./source_me.sh && cd $(VCFLIB_DIR) && HTS_LIB="$(CWD)/$(LIB_DIR)/libhts.a" HTS_INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_LDFLAGS="-L$(CWD)/$(LIB_DIR) $(START_STATIC) -lhts -ldeflate $(END_STATIC) -lpthread -lm -lbz2 -llzma -lz" $(MAKE) vcf2tsv $(FILTER)
+-
+-$(FASTAHACK_DIR)/fastahack: $(FASTAHACK_DIR)/*.c $(FASTAHACK_DIR)/*.h $(FASTAHACK_DIR)/*.cpp
+- +. ./source_me.sh && 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) $(FILTER) && cp lib/* $(CWD)/$(LIB_DIR)/ && cp obj/* $(CWD)/$(OBJ_DIR) && cp src/*.h $(CWD)/$(INC_DIR)
+
+@@ -510,16 +432,9 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/*.hpp $(DYNAMIC_DIR)/incl
+ # Otherwise we get dynamic.hpp without its deps
+ mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/* $(INC_DIR)/dynamic
+
+-$(INC_DIR)/sparsehash/sparse_hash_map: $(wildcard $(SPARSEHASH_DIR)/**/*.cc) $(wildcard $(SPARSEHASH_DIR)/**/*.h)
+- +. ./source_me.sh && cd $(SPARSEHASH_DIR) && ./autogen.sh && LDFLAGS="-L/opt/local/lib" ./configure --prefix=$(CWD) $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install
+-
+-$(INC_DIR)/sparsepp/spp.h: $(wildcard $(SPARSEHASH_DIR)/sparsepp/*.h)
++$(INC_DIR)/sparsepp/spp.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)/
+-
+ $(INC_DIR)/gfakluge.hpp: $(DEP_DIR)/gfakluge/src/gfakluge.hpp
+ +cp $(DEP_DIR)/gfakluge/src/*.hpp $(CWD)/$(INC_DIR)/ && cp $(DEP_DIR)/gfakluge/src/tinyFA/*.hpp $(CWD)/$(INC_DIR)/
+
+@@ -529,60 +444,9 @@ $(LIB_DIR)/libsonlib.a: $(CWD)/$(DEP_DIR)/sonLib/C/inc/*.h $(CWD)/$(DEP_DIR)/son
+ $(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) $(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 && 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)
+- +touch $(LIB_DIR)/libraptor2.a
+-
+-# We need rapper from Raptor for the tests
+-$(BIN_DIR)/rapper: $(LIB_DIR)/libraptor2.a
+- +cp $(RAPTOR_DIR)/build/utils/rapper $(BIN_DIR)/
+-
+-# The Raptor header needs to be newer than the library.
+-# Mac Travis managed to get an old header with a new binary.
+-$(INC_DIR)/raptor2/raptor2.h: $(LIB_DIR)/libraptor2.a $(RAPTOR_DIR)/build/*
+- +cd $(RAPTOR_DIR)/build && mkdir -p $(CWD)/$(INC_DIR)/raptor2 && cp src/*.h $(CWD)/$(INC_DIR)/raptor2
+- +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)/
+
+-# To build libvw we need to point it at our Boost, but then configure decides
+-# it needs to build vwdll, which depends on codecvt, which isn't actually
+-# shipped in the GCC 4.9 STL. So we hack vwdll AKA libvw_c_wrapper out of the
+-# build.
+-# Also, autogen.sh looks for Boost in the system, and who knows what it will do
+-# if it doesn't find it, so let it fail.
+-# Also, we need to make sure nothing about -fopenmp makes it into the build, in case we are on Clang.
+-# vw doesn't need OpenMP
+-$(LIB_DIR)/libvw.a: $(LIB_DIR)/libboost_program_options.a $(VOWPALWABBIT_DIR)/* $(VOWPALWABBIT_DIR)/vowpalwabbit/*
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && sed -i -e '/vwdll/d' Makefile.am
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./autogen.sh || true
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./configure --with-boost=$(CWD)
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) $(FILTER)
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a $(CWD)/$(LIB_DIR)/
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && mkdir -p $(CWD)/$(INC_DIR)/vowpalwabbit
+- +. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && cp vowpalwabbit/*.h $(CWD)/$(INC_DIR)/vowpalwabbit/
+-
+-$(LIB_DIR)/liballreduce.a: $(LIB_DIR)/libvw.a
+-
+-# Building Boost with GCC against libc++ on Mac doesn't work. See https://travis-ci.org/vgteam/vg/jobs/583377358
+-# So on Mac we make sure to always use Clang, even if the rest of the build uses GCC.
+-# See https://gist.github.com/jimporter/10442880
+-$(LIB_DIR)/libboost_program_options.a: $(BOOST_DIR)/libs/program_options/src/* $(BOOST_DIR)/boost/program_options/*
+-ifeq ($(shell uname -s),Darwin)
+- +. ./source_me.sh && cd $(BOOST_DIR) && ./bootstrap.sh --with-libraries=program_options --libdir=$(CWD)/$(LIB_DIR) --includedir=$(CWD)/$(INC_DIR) $(FILTER) && ./b2 --ignore-site-config --link=static toolset=clang cxxflags="-std=c++1y -stdlib=libc++" linkflags="-stdlib=libc++" install $(FILTER)
+- +. ./source_me.sh && install_name_tool -id $(CWD)/$(LIB_DIR)/libboost_program_options.dylib $(CWD)/$(LIB_DIR)/libboost_program_options.dylib
+-else
+- +. ./source_me.sh && cd $(BOOST_DIR) && ./bootstrap.sh --with-libraries=program_options --libdir=$(CWD)/$(LIB_DIR) --includedir=$(CWD)/$(INC_DIR) $(FILTER) && ./b2 --ignore-site-config --link=static cxxflags="$(CXXFLAGS)" linkflags="$(CXXFLAGS)" install $(FILTER)
+-endif
+-
+ $(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
+ +cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
+
+@@ -595,27 +459,6 @@ $(INC_DIR)/simde/x86/sse4.1.h: $(DOZEU_DIR)/simde/*.h $(DOZEU_DIR)/simde/x86/*.h
+ $(INC_DIR)/dozeu/dozeu.h: $(DOZEU_DIR)/*.h $(INC_DIR)/simde/x86/sse4.1.h
+ +mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
+
+-$(LIB_DIR)/libebl.a: $(LIB_DIR)/libelf.a
+-
+-$(LIB_DIR)/libdw.a: $(LIB_DIR)/libelf.a
+-
+-$(LIB_DIR)/libdwelf.a: $(LIB_DIR)/libelf.a
+-
+-$(LIB_DIR)/libdwfl.a: $(LIB_DIR)/libelf.a
+-
+-# We can't build elfutils from Git without "maintainer mode".
+-# There are some release-only headers or something that it complains it can't find otherwise.
+-# We also don't do a normal make and make install here because we don't want to build and install all the elfutils binaries and libasm.
+-$(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
+- +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 $(ELFUTILS_DIR) && autoreconf -i -f && ./configure --enable-maintainer-mode --prefix=$(CWD) $(FILTER)
+- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libelf && $(MAKE) clean && $(MAKE) libelf.a $(FILTER)
+- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libebl && $(MAKE) clean && $(MAKE) libebl.a $(FILTER)
+- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwfl && $(MAKE) clean && $(MAKE) libdwfl.a $(FILTER)
+- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwelf && $(MAKE) clean && $(MAKE) libdwelf.a $(FILTER)
+- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libdw && $(MAKE) clean && $(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 $(SHA1_DIR)/sha1.hpp
+ +$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
+
+@@ -623,7 +466,7 @@ $(LIB_DIR)/libfml.a: $(FERMI_DIR)/*.h $(FERMI_DIR)/*.c
+ . ./source_me.sh && cd $(FERMI_DIR) && $(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
+-$(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp $(LIB_DIR)/libhts.a
++$(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp
+ . ./source_me.sh && 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: $(INC_DIR)/BooPHF.h $(LIBBDSG_DIR)/src/*.cpp $(LIBBDSG_DIR)/include/bdsg/*.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
+@@ -783,7 +626,7 @@ clean-vg:
+ $(RM) -r $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d
+ $(RM) -f $(INC_DIR)/vg_git_version.hpp $(INC_DIR)/vg_system_version.hpp
+
+-clean: clean-rocksdb clean-vcflib
++clean:
+ $(RM) -r $(BIN_DIR)
+ $(RM) -r $(LIB_DIR)
+ $(RM) -r $(UNITTEST_OBJ_DIR)
+@@ -794,9 +637,6 @@ clean: clean-rocksdb clean-vcflib
+ $(RM) -r $(INC_DIR)
+ $(RM) -r share/
+ cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
+- cd $(DEP_DIR) && cd sparsehash && $(MAKE) clean
+- cd $(DEP_DIR) && cd htslib && $(MAKE) clean
+- cd $(DEP_DIR) && cd fastahack && $(MAKE) clean
+ cd $(DEP_DIR) && cd gcsa2 && $(MAKE) clean
+ cd $(DEP_DIR) && cd gbwt && $(MAKE) clean
+ cd $(DEP_DIR) && cd gbwtgraph && $(MAKE) clean
+@@ -804,26 +644,11 @@ clean: clean-rocksdb clean-vcflib
+ 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
+ cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
+ cd $(DEP_DIR) && cd structures && $(MAKE) clean
+- cd $(DEP_DIR) && cd jemalloc && $(MAKE) clean || true
+- cd $(DEP_DIR) && cd vowpal_wabbit && $(MAKE) clean
+ cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
+ cd $(DEP_DIR) && cd libhandlegraph && $(MAKE) clean
+ cd $(DEP_DIR) && cd libvgio && $(MAKE) clean
+- cd $(DEP_DIR) && cd raptor && cd build && find . -not \( -name '.gitignore' -or -name 'pkg.m4' \) -delete
+ # lru_cache is never built because it is header-only
+ # bash-tap is never built either
+-
+-clean-rocksdb:
+- cd $(DEP_DIR) && cd rocksdb && $(MAKE) clean
+- rm -f $(LIB_DIR)/librocksdb.a
+- rm -rf $(INC_DIR)/rocksdb/
+-
+-clean-vcflib:
+- cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
+- rm -f $(LIB_DIR)/libvcfh.a
+- cd $(INC_DIR) && rm -f BedReader.h convert.h join.h mt19937ar.h split.h Variant.h vec128int.h veclib_types.h
+diff --git a/test/Makefile b/test/Makefile
+index 5ae913873..2f9ad0286 100644
+--- a/test/Makefile
++++ b/test/Makefile
+@@ -3,22 +3,11 @@
+ CXX:=g++
+ CXXFLAGS:=-O3 -std=c++11 -fopenmp -g
+
+-vg:=../bin/vg
+-
+ all: test clean
+
+-test: build_graph $(vg) vcf2tsv fastahack
++test: build_graph $(vg) vcf2tsv
+ prove -v t
+
+-vcf2tsv:
+- cd ../deps/vcflib && $(MAKE) bin/vcf2tsv
+-
+-fastahack:
+- cd ../deps/fastahack && $(MAKE)
+-
+-$(vg):
+- cd .. && $(MAKE) bin/vg
+-
+ build_graph: build_graph.cpp
+ cd .. && . ./source_me.sh && $(MAKE) test/build_graph
+
+diff --git a/test/t/02_vg_construct.t b/test/t/02_vg_construct.t
+index 772dce140..5d87a24cb 100644
+--- a/test/t/02_vg_construct.t
++++ b/test/t/02_vg_construct.t
+@@ -75,8 +75,8 @@ rm -f fail.vg
+
+ # check that we produce a full graph
+
+-refbp=$(../deps/fastahack/fastahack -r x small/x.fa | tr -d '\n' | wc -c)
+-variantbp=$(zcat < small/x.vcf.gz | ../deps/vcflib/bin/vcf2tsv \
++refbp=$(fastahack -r x small/x.fa | tr -d '\n' | wc -c)
++variantbp=$(zcat < small/x.vcf.gz | vcf2tsv \
+ | cut -f 5,4 | tail -n+2 \
+ | awk '{ x=length($2)-length($1); if (x > 0) { print x; } else if (x == 0) { print length($2); } }' \
+ | awk '{ sum += $1 } END { print sum }')
+--
+2.28.0
+