MakefileShared

IMAGE ?= picked_group_fdr
DATA ?= $(HOME)/git/picked_group_fdr/data/lfq_example/
OUT_DIR ?= $(DATA)

LOCAL_DIR ?= /root/data
OUT_DIR_LOCAL ?= $(LOCAL_DIR)/out
MQ_EVIDENCE_FILE ?= $(LOCAL_DIR)/evidence.txt

PERC_RESULT_FILES := $(shell python3 config.py $(DATA) $(LOCAL_DIR) PERC_RESULT_FILES)
PROSIT_FLAG := $(shell python3 config.py $(DATA) $(LOCAL_DIR) PROSIT_FLAG)
DIGEST_PARAMS := $(shell python3 config.py $(DATA) $(LOCAL_DIR) DIGEST_PARAMS)
PICKED_GROUP_FDR_EXTRA_PARAMS := $(shell python3 config.py $(DATA) $(LOCAL_DIR) PICKED_GROUP_FDR_EXTRA_PARAMS)
NUM_THREADS := $(shell python3 config.py $(DATA) $(LOCAL_DIR) NUM_THREADS)

FASTA_FILE := $(notdir $(shell ls $(DATA)/*.fasta | head -n1))
INTERACTIVE := $(shell [ -t 0 ] && echo 1)
MEMORY_LIMIT ?= 4gb
CPU_LIMIT ?= 1
PERC_TEST_FDR ?= 0.01
PERC_TRAIN_FDR ?= 0.01

ifdef INTERACTIVE
	USE_TTY= -t
else
	USE_TTY=
endif

DOCKER_CMD ?= docker run -i ${USE_TTY} \
					-v "$(DATA)":/root/data/ \
					-v "$(OUT_DIR)":/root/data/out/ \
					--memory=$(MEMORY_LIMIT) \
					--cpus=$(CPU_LIMIT) \

check_fasta_file:
	echo ${FASTA_FILE}

# clean up err.out file when restarting a job
rm_err_file:
	rm -f $(DATA)err.out