From 98761eab08bf1f9590ed2acaed0c645682f53d96 Mon Sep 17 00:00:00 2001 From: Sajjad Ghaffarinasabsharabiani <ghaffas@hhu.de> Date: Tue, 9 Aug 2022 14:41:33 +0000 Subject: [PATCH] Upload New File --- networkComplexityBigg/Makefile | 186 +++++++++++++++++++++++++++++++++ 1 file changed, 186 insertions(+) create mode 100644 networkComplexityBigg/Makefile diff --git a/networkComplexityBigg/Makefile b/networkComplexityBigg/Makefile new file mode 100644 index 0000000..6ae1b9c --- /dev/null +++ b/networkComplexityBigg/Makefile @@ -0,0 +1,186 @@ +.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 + + + + + + + + + + + + + + + + + + + + -- GitLab