Update libbdsg-easy for faster PackedGraph construction

Dockerfile

@@ -15,7 +15,7 @@ ADD . /hal2vg
 WORKDIR /hal2vg
 
 # build
-RUN make clean ; make
+RUN make clean ; make -j $(nproc)
 
 # add hal2vg to the PATH
 ENV PATH /hal2vg:/hal2vg/deps/hal/bin:$PATH

Makefile

@@ -53,6 +53,11 @@ ${sonLibPath}/stPinchesAndCacti.a : ${sonLibPath}/sonLib.a ${pinchSources}
 ${libbdsgPath}/lib/libbdsg.a :
 	cd deps/libbdsg-easy && make
 
+# These archives come out of the builds above as byproducts.  Without saying so, make -j
+# on a fresh clone finds no rule for them and stops before the build that makes them runs.
+${sonLibPath}/cuTest.a : ${sonLibPath}/sonLib.a ;
+${libbdsgPath}/lib/libhandlegraph.a ${libbdsgPath}/lib/libsdsl.a ${libbdsgPath}/lib/libdivsufsort.a ${libbdsgPath}/lib/libdivsufsort64.a : ${libbdsgPath}/lib/libbdsg.a ;
+
 # jemalloc is vendored (rather than taken from the system) so that the static release
 # binaries are self contained and always get the same allocator: its size classes are
 # what make the pinch graph cheap, so a different version could quietly change how much
@@ -107,7 +112,7 @@ count-vg-hap-cov : count-vg-hap-cov.o ${basicLibsDependencies}
 	${cpp} ${CXXFLAGS} -fopenmp -pthread count-vg-hap-cov.o  ${basicLibs}  -o count-vg-hap-cov
 
 test :
-	make
+	${MAKE}
 	${MAKE} test-only
 
 # run the tests against whatever binaries are already sitting in the tree.  the release

build-tools/makeBinRelease

@@ -32,15 +32,17 @@ git submodule update --init --recursive
 # todo: update / figure out / remove hack:
 cp ./build-tools/CMakeLists.txt ./deps/libbdsg-easy/deps/libhandlegraph/CMakeLists.txt
 
+jobs=$(nproc)
+
 if [ $(man gcc | grep nehalem | wc -l) -ge 1 ]
 then
 	 # attempt to increase portability by using older architecture
 	 # this make/sed/make thing is a hack to get around a linking error that just cropped up
-	 CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make static || true
+	 CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make -j ${jobs} static || true
 	 sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g"	 
 	 CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make check-static
 else
-	 make static || true
+	 make -j ${jobs} static || true
 	 sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g"
 	 make check-static
 fi