code_review/Makefile at master · aj-kozik/code_review · GitHub

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REFS = data/references
FIGS = results/figures
TABLES = results/tables
PROC = data/process
FINAL = submission/
CODE = code/learning


################################################################################
#
# Part 1: Retrieve the subsampled shared file and metadata files that Marc Sze
# published in https://github.com/SchlossLab/Sze_CRCMetaAnalysis_mBio_2018
#
#	Copy from Github
#
################################################################################

data/baxter.0.03.subsample.shared\
data/metadata.tsv	:	code/learning/load_datasets.batch
	bash code/learning/load_datasets.batch

################################################################################
#
# Part 2: Model analysis in R
#
#	Run scripts to perform all the models on the dataset and generate AUC values
#
################################################################################

$(PROC)/combined_all_imp_features_results_L2_Logistic_Regression.csv\
$(PROC)/combined_all_hp_results_L2_Logistic_Regression.csv\
$(PROC)/combined_best_hp_results_L2_Logistic_Regression.csv	:	data/baxter.0.03.subsample.shared\
														data/metadata.tsv\
														$(CODE)/generateAUCs.R\
														$(CODE)/model_pipeline.R\
														$(CODE)/model_interpret.R\
														$(CODE)/main.R\
														$(CODE)/model_selection.R\
														code/cat_csv_files.sh\
														L2_Logistic_Regression.pbs
			qsub L2_Logistic_Regression.pbs

$(PROC)/combined_all_imp_features_results_L2_Linear_SVM.csv\
$(PROC)/combined_all_hp_results_L2_Linear_SVM.csv\
$(PROC)/combined_best_hp_results_L2_Linear_SVM.csv	:	data/baxter.0.03.subsample.shared\
														data/metadata.tsv\
														$(CODE)/generateAUCs.R\
														$(CODE)/model_pipeline.R\
														$(CODE)/model_interpret.R\
														$(CODE)/main.R\
														$(CODE)/model_selection.R\
														code/cat_csv_files.sh\
														L2_Linear_SVM.pbs
			qsub L2_Linear_SVM.pbs
			bash code/test_sleep.sh
			bash code/cat_csv_files.sh


################################################################################
#
# Part 3: Figure and table generation
#
#	Run scripts to generate figures and tables
#
################################################################################

# Figure 1 shows the generalization performance of all the models tested.
$(FIGS)/Figure_1.pdf :	$(CODE)/functions.R\
						$(CODE)/Figure1.R\
						$(PROC)/combined_best_hp_results_L2_Logistic_Regression.csv\
						$(PROC)/combined_best_hp_results_L2_Linear_SVM.csv
	Rscript $(CODE)/Figure1.R