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Makefile
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## Cameron Palmer, 19 May 2020
## Primary entry point for PLCO analysis pipeline
##
include Makefile.config
MAKEFILE_CONFIG_LOCATION := $(shell pwd)/Makefile.config
export
.SECONDEXPANSION:
.PHONY: all $(SUPPORTED_METHODS) bgen meta metal meta-analysis metaanalysis cleaned-chips-by-ancestry ancestry relatedness ldsc 1KG_files fastgwa-grm ldscores plotting flat-dosages globus
all: meta
plotting: #$(SUPPORTED_METHODS) meta
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.plotting
## meta-analysis targets
## this understands EXCLUDE_{METHOD} parameters to restrict the meta to certain analyses over others
META_ALIASES := meta-analysis metaanalysis metal meta
$(META_ALIASES): ##$(SUPPORTED_METHODS)
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.metal
$(addsuffix -saige,$(META_ALIASES)):
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.metal EXCLUDE_BOLTLMM=1 EXCLUDE_FASTGWA=1
$(addsuffix -fastgwa,$(META_ALIASES)):
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.metal EXCLUDE_BOLTLMM=1 EXCLUDE_SAIGE=1
$(addsuffix -boltlmm,$(META_ALIASES)):
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.metal EXCLUDE_FASTGWA=1 EXCLUDE_SAIGE=1
fastgwa: fastgwa-grm
$(SUPPORTED_METHODS): #cleaned-chips-by-ancestry ldsc
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.$@
bgen:
$(MAKE) -C $(BGEN_OUTPUT_DIR)
fastgwa-grm: cleaned-chips-by-ancestry
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.fastgwa.grm
cleaned-chips-by-ancestry: ancestry
$(MAKE) -C $(CLEANED_CHIP_OUTPUT_DIR)
ancestry: relatedness
$(MAKE) -C $(ANCESTRY_OUTPUT_DIR)
relatedness:
$(MAKE) -C $(RELATEDNESS_OUTPUT_DIR)
ldsc: 1KG_files
$(MAKE) -C $(LDSC_OUTPUT_DIR)
1KG_files:
$(MAKE) -C $(KG_REFERENCE_INPUT_DIR)
ldscores: ##$(SUPPORTED_METHODS) meta
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.$@
globus: # meta
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.$@
## TESTING CONTROLLERS
.PHONY: check bgen-check relatedness-check ancestry-check cleaned-chips-by-ancestry-check fastgwa-check boltlmm-check fastgwa-grm-check ldscores-check saige-check config-check meta-check ldsc-check globus-check
check: bgen-check relatedness-check ancestry-check cleaned-chips-by-ancestry-check fastgwa-check boltlmm-check fastgwa-grm-check ldscores-check saige-check config-check meta-check ldsc-check globus-check
bgen-check:
$(MAKE) -C $(BGEN_OUTPUT_DIR) check FILTERED_DOSAGE_DATA=$(FILTERED_IMPUTED_INPUT_DIR)
relatedness-check:
$(MAKE) -C $(RELATEDNESS_OUTPUT_DIR) check CHIPS="$(sort $(foreach chip,$(PLATFORMS),$(firstword $(subst _, ,$(chip)))))"
ancestry-check:
$(MAKE) -C $(ANCESTRY_OUTPUT_DIR) check CHIPS="$(sort $(foreach chip,$(PLATFORMS),$(firstword $(subst _, ,$(chip)))))"
cleaned-chips-by-ancestry-check:
$(MAKE) -C $(CLEANED_CHIP_OUTPUT_DIR) check CHIPS="$(sort $(foreach chip,$(PLATFORMS),$(firstword $(subst _, ,$(chip)))))" ANCESTRY_DIR=$(ANCESTRY_OUTPUT_DIR) ANCESTRY_NAMES="$(CLEANED_ANCESTRY_NAMES)"
boltlmm-check: config-check
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.check $@ CONFIG_DIR=$(CONFIG_INPUT_DIR) CHIP_DIR=$(CLEANED_CHIP_OUTPUT_DIR) IMPUTED_DIR=$(BGEN_OUTPUT_DIR) RESULTS_DIR=$(RESULT_OUTPUT_DIR) MINIMUM_SUBJECTS=$(BOLTLMM_MINIMUM_VALID_SUBJECT_COUNT)
fastgwa-check: config-check
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.check $@ CONFIG_DIR=$(CONFIG_INPUT_DIR) CHIP_DIR=$(CLEANED_CHIP_OUTPUT_DIR) IMPUTED_DIR=$(BGEN_OUTPUT_DIR) RESULTS_DIR=$(RESULT_OUTPUT_DIR) MINIMUM_SUBJECTS=$(FASTGWA_MINIMUM_VALID_SUBJECT_COUNT)
saige-check: config-check
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.check $@ CONFIG_DIR=$(CONFIG_INPUT_DIR) CHIP_DIR=$(CLEANED_CHIP_OUTPUT_DIR) IMPUTED_DIR=$(BGEN_OUTPUT_DIR) RESULTS_DIR=$(RESULT_OUTPUT_DIR) MINIMUM_SUBJECTS=$(SAIGE_MINIMUM_VALID_SUBJECT_COUNT) MINIMUM_CASES=$(MINIMUM_VALID_CASE_COUNT)
config-check:
$(MAKE) -C $(CONFIG_INPUT_DIR) PHENOTYPE_FILE=$(PHENOTYPE_FILENAME) GET_SINGLE_YAML_ENTRY=$(GET_SINGLE_YAML_ENTRY)
meta-check:
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.check $@ CONFIG_DIR=$(CONFIG_INPUT_DIR) RESULTS_DIR=$(RESULT_OUTPUT_DIR)
1KG_files-check:
$(MAKE) -C $(KG_REFERENCE_INPUT_DIR) check KG_PREFIX=$(KG_GENOTYPES_PREFIX) KG_SUFFIX=$(KG_GENOTYPES_SUFFIX)
ldsc-check:
$(MAKE) -C $(LDSC_OUTPUT_DIR) check
globus-check:
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.check $@ GLOBUS_DIR=$(GLOBUS_OUTPUT_DIR)
## CLEANING INTERMEDIATES
bgen-secondary-clean:
$(MAKE) -C $(BGEN_OUTPUT_DIR) secondary-clean
$(addsuffix -secondary-clean,$(SUPPORTED_METHODS)):
$(MAKE) -C $(SHARED_MAKEFILES) -f Makefile.$(subst -secondary-clean,,$@) secondary-clean