Reduce the amount of make output and speed up the build

The build logs were going over 4MB so Travis was failing the
build. Now building the dependencies only produces output if the build fails.

Dockerfile

@@ -1,13 +1,14 @@
 FROM ubuntu:16.04
 
-
 RUN apt-get update && apt-get install -y git gcc g++ build-essential python-dev zlib1g-dev libkyototycoon-dev libtokyocabinet-dev libkyotocabinet-dev wget valgrind libbz2-dev
 
+ENV kyotoTycoonIncl -I/usr/include -DHAVE_KYOTO_TYCOON=1 -fpermissive
+ENV kyotoTycoonLib -L/usr/lib -Wl,-rpath,/usr/lib -lkyototycoon -lkyotocabinet -lz -lbz2 -lpthread -lm -lstdc++
 RUN mkdir -p /home/cactus
 
 COPY . /home/cactus
 
+RUN cd /home/cactus && make deps
 RUN cd /home/cactus && make
-
 RUN mkdir /data
 WORKDIR /data

Makefile

@@ -9,20 +9,6 @@ runtime_fullpath = $(realpath runtime)
 
 export sonLibRootPath = ${PWD}/submodules/sonLib
 
-libtokyocabinet = ${PWD}/submodules/tokyocabinet/libtokyocabinet.a
-libkyototycoon = ${PWD}/submodules/kyototycoon/libkyototycoon.a
-libkyotocabinet = ${PWD}/submodules/kyotocabinet/libkyotocabinet.a
-
-
-export tcPrefix = $(PWD)/submodules/tokyocabinet
-export tokyoCabinetIncl = -I ${tcPrefix}/include -DHAVE_TOKYO_CABINET=1
-export tokyoCabinetLib = -L${tcPrefix}/lib -Wl,-Bstatic -ltokyocabinet -Wl,-Bdynamic -lz -lpthread -lm
-
-export kcPrefix =$(PWD)/submodules/kyotocabinet
-export ttPrefix =$(PWD)/submodules/kyototycoon
-export kyotoTycoonIncl = -I${kcPrefix}/include -I${ttPrefix}/include -DHAVE_KYOTO_TYCOON=1 -I$(PWD)/zlib/include -fpermissive
-export kyotoTycoonLib = -L${ttPrefix}/lib -L${kcPrefix}/lib -Wl,-Bstatic -lkyototycoon -lkyotocabinet -Wl,-Bdynamic -lz -lpthread -lm -lstdc++
-
 libSonLib = ${PWD}/submodules/sonLib/sonLib.a
 libPinchesAndCacti = ${PWD}/submodules/sonLib/lib/stPinchesAndCacti.a
 libCPecan = ${PWD}/submodules/sonLib/lib/cPecanLib.a
@@ -31,15 +17,16 @@ libMatchingAndOrdering = ${PWD}/submodules/sonLib/lib/matchingAndOrdering.a
 halAppendCactusSubtree = ${PWD}/submodules/cactus2hal/bin/halAppendCactusSubtree
 h5c++ = ${PWD}/submodules/hdf5/bin/h5c++
 
-.PHONY: all %.all clean %.clean
-
-all : ${libSonLib} ${libPinchesAndCacti} ${libMatchingAndOrdering} ${libCPecan} ${modules:%=all.%} ${halAppendCactusSubtree}
+.PHONY: all all.% clean clean.% selfClean
 
+all: deps ${modules:%=all.%} ${halAppendCactusSubtree}
 
 all.%:
 	cd $* && make all
 
-clean:  ${modules:%=clean.%}
+deps: ${libSonLib} ${libPinchesAndCacti} ${libMatchingAndOrdering} ${libCPecan} hdf5Rule halRule
+
+selfClean:  ${modules:%=clean.%}
 	rm -rf lib/*.h bin/*.dSYM
 
 clean.%:
@@ -48,7 +35,6 @@ clean.%:
 test: all
 	python allTests.py
 
-
 build_output: Dockerfile
 	mkdir -p ${runtime_fullpath}/tools
 	docker build -t cactusbuild:${tag} .
@@ -58,63 +44,52 @@ build_output: Dockerfile
 	docker rmi -f cactusbuild:${tag}
 
 docker: build_output runtime/Dockerfile
-	docker rmi -f ${name}:latest
+	-docker rmi -f ${name}:latest
 	docker build -t ${name}:${tag} ./runtime/ --build-arg CACTUS_COMMIT=${git_commit}
 	docker tag ${name}:${tag} ${name}:latest
 
 push: docker
 	# Requires ~/.dockercfg
 	docker push ${name}
 
-
-${libSonLib}: ${libkyotocabinet} ${libtokyocabinet} ${libkyototycoon}
-	cd ${PWD}/submodules/sonLib && make
+${libSonLib}:
+	@echo "Building dependency sonLib"
+	@cd ${PWD}/submodules/sonLib && (output=$$(make 2>&1) || (echo "$$output"; exit 1))
 
 sonLibRule: ${libSonLib}
 
-tokyocabinetRule: ${libtokyocabinet}
-
-kyototycoonRule: ${libkyototycoon}
-
-kyotocabinetRule: ${libkyotocabinet}
-
-${libtokyocabinet}:
-	cd ${PWD}/submodules/tokyocabinet && ./configure --prefix=${PWD}/submodules/tokyocabinet --enable-static --disable-shared --disable-bzip && make && make install
-
-${libkyototycoon}:
-	cd ${PWD}/submodules/kyototycoon && ./configure --prefix=${PWD}/submodules/kyototycoon --enable-static --disable-shared --with-kc=${PWD}/submodules/kyotocabinet && make && make install
-
-${libkyotocabinet}:
-	cd ${PWD}/submodules/kyotocabinet && ./configure --prefix=${PWD}/submodules/kyotocabinet --enable-static --disable-shared && make && make install
-
-
-${libPinchesAndCacti}:
-	cd ${PWD}/submodules/pinchesAndCacti && make
+${libPinchesAndCacti}: ${libSonLib}
+	@echo "Building dependency pinchesAndCacti"
+	@cd ${PWD}/submodules/pinchesAndCacti && (output=`make 2>&1` || (echo "$$output"; exit 1))
 
-${libMatchingAndOrdering}:
-	cd ${PWD}/submodules/matchingAndOrdering && make
+${libMatchingAndOrdering}: ${libSonLib}
+	@echo "Building dependency matchingAndOrdering"
+	@cd ${PWD}/submodules/matchingAndOrdering && (output=`make 2>&1` || (echo "$$output"; exit 1))
 
-${libCPecan}:
-	cd ${PWD}/submodules/cPecan && make
+${libCPecan}: ${libSonLib}
+	@echo "Building dependency cPecan"
+	@cd ${PWD}/submodules/cPecan && (output=`make 2>&1` || (echo "$$output"; exit 1))
 
-${halAppendCactusSubtree}: ${h5c++} halRule
-	cd ${PWD}/submodules/cactus2hal && PATH=${PWD}/submodules/hdf5/bin:$(PATH) make
+${halAppendCactusSubtree}: ${h5c++} halRule all.api
+	@echo "Building dependency cactus2hal"
+	@cd ${PWD}/submodules/cactus2hal && (PATH=${PWD}/submodules/hdf5/bin:$(PATH) output=`make 2>&1` || (echo "$$output"; exit 1))
 
 hdf5Rule: ${h5c++}
 
 ${h5c++}:
-	cd ${PWD}/submodules/hdf5 &&./configure --prefix=$(PWD)/submodules/hdf5 --enable-cxx && CFLAGS=-std=c99 make -e && make install
+	@echo "Building dependency hdf5"
+	@cd ${PWD}/submodules/hdf5 && (output=`(./configure --prefix=$(PWD)/submodules/hdf5 --enable-cxx && CFLAGS=-std=c99 make -e && make install) 2>&1` || (echo "$$output"; exit 1))
 
-halRule:
-	cd ${PWD}/submodules/hal && PATH=${PWD}/submodules/hdf5/bin:$(PATH) make
+halRule: ${h5c++} ${libSonLib}
+	@echo "Building dependency hal"
+	@cd ${PWD}/submodules/hal && (PATH=${PWD}/submodules/hdf5/bin:$(PATH) output=`make 2>&1` || (echo "$$output"; exit 1))
 
-ucscClean:
-	make clean
+ucscClean: selfClean
 	cd ${PWD}/submodules/sonLib && make clean
 	cd ${PWD}/submodules/pinchesAndCacti && make clean
 	cd ${PWD}/submodules/matchingAndOrdering && make clean
 
-clean: ucscClean
+clean: ucscClean selfClean
 	cd ${PWD}/submodules/kyotocabinet && make clean
 	cd ${PWD}/submodules/kyototycoon && make clean
 	cd ${PWD}/submodules/tokyocabinet && make clean

include.mk

@@ -6,10 +6,10 @@ libPath=${rootPath}lib/
 sonLibRootPath?=${rootPath}/../sonLib
 sonLibPath=${sonLibRootPath}/lib
 
-include  ${sonLibRootPath}/include.mk
+include ${sonLibRootPath}/include.mk
 
 dataSetsPath=/Users/benedictpaten/Dropbox/Documents/work/myPapers/genomeCactusPaper/dataSets
 
-cflags += -I ${sonLibPath} ${tokyoCabinetIncl} ${kyotoTycoonIncl} ${mysqlIncl} ${pgsqlIncl}
+cflags += -I ${sonLibPath}
 basicLibs = ${sonLibPath}/sonLib.a ${sonLibPath}/cuTest.a ${dblibs}
 basicLibsDependencies = ${sonLibPath}/sonLib.a ${sonLibPath}/cuTest.a