Makefile

PICKEDGROUPFDR_DIR := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
include $(PICKEDGROUPFDR_DIR)MakefileShared
include $(PICKEDGROUPFDR_DIR)MakefileFigures

dependencies:
	git config --global credential.helper cache

registry:
	docker login gitlab.lrz.de:5005
	docker build -t gitlab.lrz.de:5005/proteomics/picked_group_fdr .
	docker push gitlab.lrz.de:5005/proteomics/picked_group_fdr

jump: 
	$(DOCKER_CMD) \
		$(IMAGE) bash

test_for_release: test integration_test pipeline_test system_test

test:
	python3 -m pytest --cov=picked_group_fdr --cov-report html --cov-report term tests/unit_tests

system_test:
	tests/system_tests/test_all.sh

integration_test:
	python3 -um picked_group_fdr --mq_evidence $(DATA)/evidence.txt \
		--fasta $(DATA)/db.fasta \
		--enzyme trypsinp \
		--min-length 6 \
		--protein_groups_out ${DATA}/proteinGroups.txt \
		--method picked_protein_group_mq_input \
		--do_quant

fragpipe_test:
	cd data/fragpipe_example && ./run_picked_group_fdr.sh

sage_test:
	cd data/sage_example && ./run_picked_group_fdr.sh

rm_previous_results:
	rm -rf $(DATA)/percolator

# testing the docker pipeline without docker
pipeline_test: DOCKER_CMD=
pipeline_test: IMAGE=
pipeline_test: LOCAL_DIR=$(DATA)
pipeline_test: OUT_DIR_LOCAL=$(DATA)
pipeline_test: rm_previous_results all

performance:
	python3 -m pytest -s tests/performance_tests/test_lfq.py

# can be visualized with snakeviz -H 0.0.0.0 -s program.prof
performance_cprofile:
	python3 -m cProfile -o program.prof tests/performance_tests/test_lfq.py

# need to run "pip install ." before kernprof to reflect the changes in the package
line_profiler_lfq:
	kernprof -lv tests/performance_tests/test_lfq.py

# can be plotted with mprof plot
memory_profile:
	mprof run --include-children --backend psutil_pss python3 -u tests/performance_tests/test_lfq.py | ts '[%H:%M:%.S]'

# --no-cache
build: dependencies
	docker build -f Dockerfile -t $(IMAGE) .

bootstrap: DATA=/root/data
bootstrap:
	bash -c "cp /root/{config.py,Makefile*} $(LOCAL_DIR)"

####################################################################################
### Pipeline including recalculation of PEPs by mokapot (=percolator for Python) ###
####################################################################################

prepayload_setup_create_folder: rm_err_file
	$(DOCKER_CMD) \
		$(IMAGE) mkdir -p -m 777 $(OUT_DIR_LOCAL)/percolator || (echo "1" > $(DATA)err.out; exit 1)

# inside the docker, we need to call python through bash because the default shell (/bin/sh) results in a permission denied error
tab: prepayload_setup_create_folder
ifeq ($(PROSIT_FLAG),)
	$(DOCKER_CMD) \
		$(IMAGE) bash -c "python3 -u -m picked_group_fdr.pipeline.andromeda2pin \
			$(MQ_EVIDENCE_FILE) \
			--outputTab $(OUT_DIR_LOCAL)/percolator/andromeda.tab \
			--databases \"$(LOCAL_DIR)/$(FASTA_FILE)\" \
			$(DIGEST_PARAMS) \
			> $(OUT_DIR_LOCAL)/percolator/andromeda2pin.log"
endif

# calculating PEPs with Triqler within mokapot is very slow with OMP multithreading, so set this to 1 for now
percolator: tab
ifeq ($(PROSIT_FLAG),)
	$(DOCKER_CMD) \
		$(IMAGE) bash -c "OMP_NUM_THREADS=1 python3 -u -m picked_group_fdr.pipeline.run_mokapot \
			$(PERC_TEST_FDR) $(PERC_TRAIN_FDR) $(OUT_DIR_LOCAL)/percolator $(NUM_THREADS)"
endif

update_evidence: percolator
	$(DOCKER_CMD) \
		$(IMAGE) bash -c "python3 -u -m picked_group_fdr.pipeline.update_evidence_from_pout \
			--mq_evidence $(MQ_EVIDENCE_FILE) \
			--perc_results $(PERC_RESULT_FILES) \
			--mq_evidence_out $(OUT_DIR_LOCAL)/percolator/evidence.txt \
			$(PROSIT_FLAG) \
			> $(OUT_DIR_LOCAL)/percolator/update_evidence.log"

picked_fdr: update_evidence
	$(DOCKER_CMD) \
		$(IMAGE) bash -c "OMP_DYNAMIC=FALSE OMP_NUM_THREADS=1 python3 -u -m picked_group_fdr \
			--mq_evidence $(OUT_DIR_LOCAL)/percolator/evidence.txt \
			--protein_groups_out $(OUT_DIR_LOCAL)/percolator/proteinGroups.txt \
			--do_quant \
			--fasta \"$(LOCAL_DIR)/$(FASTA_FILE)\" \
			--methods picked_protein_group_mq_input \
			--num_threads $(NUM_THREADS) \
			$(DIGEST_PARAMS) \
			$(PICKED_GROUP_FDR_EXTRA_PARAMS) \
			> $(OUT_DIR_LOCAL)/percolator/proteinGroups.log"

picked_fdr_gene_level: picked_fdr
	$(DOCKER_CMD) \
		$(IMAGE) bash -c "OMP_DYNAMIC=FALSE OMP_NUM_THREADS=1 python3 -u -m picked_group_fdr \
			--mq_evidence $(OUT_DIR_LOCAL)/percolator/evidence.txt \
			--protein_groups_out $(OUT_DIR_LOCAL)/percolator/geneGroups.txt \
			--do_quant \
			--gene_level \
			--fasta \"$(LOCAL_DIR)/$(FASTA_FILE)\" \
			--methods picked_protein_group_mq_input \
			--num_threads $(NUM_THREADS) \
			$(DIGEST_PARAMS) \
			$(PICKED_GROUP_FDR_EXTRA_PARAMS) \
			--suppress_missing_peptide_warning \
			> $(OUT_DIR_LOCAL)/percolator/geneGroups.log"

# by popular demand: also produce an evidence.txt and proteinGroups.txt filtered at 1% FDR
filter_results: picked_fdr_gene_level
	$(DOCKER_CMD) \
		$(IMAGE) bash -c "OMP_DYNAMIC=FALSE OMP_NUM_THREADS=1 python3 -u -m picked_group_fdr.pipeline.filter_fdr_maxquant \
			--mq_msms $(OUT_DIR_LOCAL)/percolator/evidence.txt \
			--mq_msms_out $(OUT_DIR_LOCAL)/percolator/evidence_fdr0.01.txt \
			--mq_protein_groups $(OUT_DIR_LOCAL)/percolator/proteinGroups.txt \
			--mq_protein_groups_out $(OUT_DIR_LOCAL)/percolator/proteinGroups_fdr0.01.txt \
			--fdr_cutoff 0.01 \
			--psm_level_fdr \
			> $(OUT_DIR_LOCAL)/percolator/filter_results.log"

filter_results_gene_level: filter_results
	$(DOCKER_CMD) \
		$(IMAGE) bash -c "python3 -u -m picked_group_fdr.pipeline.filter_fdr_maxquant \
			--mq_protein_groups $(OUT_DIR_LOCAL)/percolator/geneGroups.txt \
			--mq_protein_groups_out $(OUT_DIR_LOCAL)/percolator/geneGroups_fdr0.01.txt \
			--fdr_cutoff 0.01 \
			--psm_level_fdr \
			> $(OUT_DIR_LOCAL)/percolator/filter_results_gene_level.log"

compress: filter_results_gene_level
	zip -j -r -9 "$(OUT_DIR)/results.zip" "$(OUT_DIR)/percolator/"

all: compress




# run this step manually if mokapot runs out of memory, tested with percolator 3.05
percolator_subset_training: 
	percolator --weights $(OUT_DIR_LOCAL)/percolator/andromeda.weights.txt -Y \
		--testFDR $(PERC_TEST_FDR) \
		--trainFDR $(PERC_TRAIN_FDR) \
		--subset-max-train 10000000 \
		--results-psms $(OUT_DIR_LOCAL)/percolator/andromeda.mokapot.psms.txt \
		--decoy-results-psms $(OUT_DIR_LOCAL)/percolator/andromeda.mokapot.decoy.psms.txt \
		--results-peptides $(OUT_DIR_LOCAL)/percolator/andromeda.mokapot.peptides.txt \
		--decoy-results-peptides $(OUT_DIR_LOCAL)/percolator/andromeda.mokapot.decoy.peptides.txt \
		$(OUT_DIR_LOCAL)/percolator/andromeda.tab 2>&1 | tee $(OUT_DIR_LOCAL)/percolator/andromeda.log