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networkComplexityBigg/Makefile

+.PHONY : all
+.SUFFIXES:
+.SECONDARY: 
+MAKEFLAGS += --no-builtin-rules
+CC=
+CXX=
+SHELL:=/bin/bash -o pipefail
+
+CORES=7
+
+# task dependency files (*.d) are orderd sequential.
+# targets below are ordered in reverse
+all: 	download.d\
+		readModels.d\
+		modelsCheck.d\
+		buildModel.d\
+		analyseUniversalModel.d\
+		convertMedia.d\
+		mediaMapping/mediaBiGG.Rdata\
+		models/universalBiGG.ver1.2.Rdata\
+		models/universalBiGG.ver1.1.Rdata\
+		models/universalBiGG.ver1.Rdata\
+		compGrowth.d\
+		models/universalMNX.ver2.Rdata\
+		imbalanceRemovalByBlocking.d\
+		massBalanceCheck.d\
+		modelTable.d\
+		analyseEGC.d\
+		analyseFBA.d\
+		analyseARM.d\
+		analyseCross.d\
+		innovationIndex.Rdata
+
+clean: rm -f *.d
+
+
+#.d: .d
+#	@echo ">>> "
+#	@rm -f .out
+#	exit 1 |& tee -a ../.out
+#	touch .d
+
+################################################################################
+innovationIndex.Rdata: analyseCross.d
+analyseCross.d: analyseARM.d envirDist/crossdata/*.Rdata
+	@echo ">>> analysing cross fba data"
+	@rm -f analyseCross.out
+	cd envirDist && ./analyseCross.R |& tee -a ../analyseCross.out
+	touch analyseCross.d
+################################################################################
+mergedResults.Rdata result.Rdata: analyseARM.d
+analyseARM.d: envirDist/compareDf.Rdata envirDist/envirdata/*.Rdata modelTable.d
+	@echo ">>> analysing envirDist data and creating plots"
+	@rm -f analyseARM.out
+	cd envirDist && ./analyseARM.R |& tee -a ../analyseARM.out
+	touch analyseARM.d
+################################################################################
+modelTable.d: dataAnalysis/tax_report.txt sourceData/modelList.tsv dataAnalysis/updateModelTable.R
+	@echo ">>> updating model table"
+	@rm -f modelTable.out
+	cd dataAnalysis && ./updateModelTable.R |& tee -a ../modelTable.out
+	touch modelTable.d
+################################################################################
+envirDist/compareDf.Rdata: analyseFBA.d
+analyseFBA.d: analyseEGC.d models/universalMNX.ver2.Rdata envirDist/analyseFBA.R
+	@echo ">>> analysing fba results"
+	@rm -f analyseFBA.out
+	cd envirDist && ./analyseFBA.R |& tee -a ../analyseFBA.out
+	touch analyseFBA.d
+################################################################################
+# egcRemoval has to be done on a compute node, here only results will be summarized
+models/universalMNX.ver2.Rdata: analyseEGC.d qc/testGrowth.R
+analyseEGC.d: imbalanceRemovalByBlocking.d models/universalBiGG.ver1.2.Rdata energyGeneratingCycleRemoval/results/*.Rdata energyGeneratingCycleRemoval/analyseResults.R compGrowth.d
+	@echo ">>> analysing EGC removal data"
+	@rm -f analyseEGC.out testGrowth.out
+	@rm -f energyGeneratingCycleRemoval/*.pdf
+	cd energyGeneratingCycleRemoval && ./analyseResults.R |& tee -a ../.out
+	cd qc && ./testGrowth.R |& tee -a ../testGrowth.out
+	touch analyseEGC.d
+################################################################################
+# mass balances removal by finding blocked reactions.
+imbalanceRemovalByBlocking.d: massBalanceCheck.d models/universalBiGG.ver1.1.Rdata imbalanceRemoval/imbalanceRemovalByBlocking.R
+	@echo ">>> mass imbalances removal by finding blocked reactions"
+	@rm -f imbalanceRemovalByBlocking.out
+	cd imbalanceRemoval && ./imbalanceRemovalByBlocking.R |& tee -a ../imbalanceRemovalByBlocking.out
+	touch imbalanceRemovalByBlocking.d
+################################################################################
+# mass balance check
+massBalanceCheck.d: convertMedia.d models/universalBiGG.ver1.1.Rdata massBalanceCheck/massBalanceCheck.R
+	@echo ">>> mass balance check"
+	@rm -f massBalanceCheck.out
+	cd massBalanceCheck && ./massBalanceCheck.R |& tee -a ../massBalanceCheck.out
+	touch massBalanceCheck.d
+
+################################################################################
+# compare growth of previous seed adaption to latest bigg version
+compGrowth.d: convertMedia.d analyseUniversalModel.d convertMedia/mediaBiGG.Rdata models/universalBiGG.ver1.1.Rdata
+	@echo ">>> comparing bigg model to growth from previous model"
+	@rm -f compGrowth.out
+	cd qc && ./compGrowth.R |& tee -a ../.out
+	touch compGrowth.d
+################################################################################
+#map media from seed namespace to BiGG namespace
+mediaMapping/mediaBiGG.Rdata: convertMedia.d
+convertMedia.d: analyseUniversalModel.d\
+				models/universalBiGG.ver1.1.Rdata\
+				convertMedia/convertMedia.R
+	@echo ">>> converting media from seed to bigg"
+	@rm -f convertMedia.out
+	cd convertMedia && ./convertMedia.R |& tee -a ../convertMedia.out
+	cd convertMedia && ./generateRandomMedia.R |& tee -a ../convertMedia.out
+	cd convertMedia && ./mdsMedia.R |& tee -a ../convertMedia.out
+	touch convertMedia.d
+################################################################################
+#analysemodel
+models/universalBiGG.ver1.1.Rdata: analyseUniversalModel.d
+analyseUniversalModel.d: 	buildModel/analyseUniversalModel.R\
+							models/universalBiGG.ver1.Rdata\
+							buildModel/selectBiomassTable_mod.csv\
+							buildModel.d
+	@echo ">>> running analyseUniversalModel"
+	@rm -f analyseUniversalModel.out
+	cd buildModel && ./analyseUniversalModel.R |& tee -a ../analyseUniversalModel.out
+	touch analyseUniversalModel.d
+
+################################################################################
+# build model
+models/universalBiGG.ver1.Rdata: buildModel.d
+buildModel.d: 	buildModel/addDefaultBOF.R\
+				buildModel/buildModel.R\
+				modelsCheck.d
+	@echo ">>> running buildModel"
+	@rm -f buildModel.out
+	cd buildModel && ./buildModel.R |& tee -a ../buildModel.out
+	touch buildModel.d
+
+################################################################################
+modelsCheck.d: 	modelsCheck/modelsCheck.R\
+				sourceData/models.Rdata\
+				sourceData/excludeModels.txt\
+				download.d\
+				readModels.d
+	@echo ">>> running modelsCheck"
+	@rm -f modelsCheck.out
+	cd modelsCheck && exec ./modelsCheck.R |& tee -a ../modelsCheck.out
+	touch modelsCheck.d
+	
+
+################################################################################
+sourceData/models.Rdata: readModels.d
+
+readModels.d: download.d
+	@echo ">>> reading models"
+	rm -rf readModels.out
+	cd modelsCheck && ./readModels.R |& tee ../readModels.out
+	touch readModels.d
+
+################################################################################
+
+download.d:	
+	@echo ">>> fetching models from Bigg Database"
+	cd download && ./getModels.py |& tee ../sourceData/modelList_source.tsv
+	cd sourceData && cat modelList_source.tsv buchnera.tsv > modelList.tsv
+	cd sourceData && wget -N http://bigg.ucsd.edu/static/namespace/bigg_models_reactions.txt
+	cd sourceData && wget -N http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt
+	touch download.d
+	
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