Makefile

help:
	@echo "Main targets:"
	@echo "  test            - perform function tests." 
	@echo "  test_tools      - perform tool tests."
	@echo "  test_tools_db   - perform DB tool tests." 
	@echo "  test_pipeline_a - perform DNA amplicon pipeline test (Haloplex HBOC v5)." 
	@echo "  test_pipeline_x - perform DNA shotgun pipeline test."
	@echo "  test_pipeline_t - perform DNA trio pipeline test."
	@echo "  test_pipeline_m - perform DNA multi-sample pipeline test."
	@echo "  test_pipeline_s - perform DNA somatic pipeline test."
	@echo "  test_pipeline_r - perform RNA pipeline test."
	@echo "  test_all        - perform all tests."
	
	@echo "" 
	@echo "Auxilary targets:"
	@echo "  find_missing_tests - Checks for tools that do not have a test."
	@echo "  todos              - Checks for todos in the code"

test: dummy
	@cd test && find . -name "test_*.php"  | xargs -l1000 php execute_tests.php ALL 

test_tools: dummy
	@cd test && find . -name "tool_test_*.php" | xargs -l1000 php execute_tests.php ALL 

test_tools_primer: dummy
	@cd test && find . -name "tool_test_*.php" | xargs -l1000 php execute_tests.php Primer 

test_tools_ngs: dummy
	@cd test && find . -name "tool_test_*.php" | xargs -l1000 php execute_tests.php NGS

test_tools_tools: dummy
	@cd test && find . -name "tool_test_*.php" | xargs -l1000 php execute_tests.php Tools  	

test_tools_db:
	@cd test && find . -name "tool_test_*.php" | grep tool_test_db | xargs -l1000 php execute_tests.php NGS 

test_pipeline_a: dummy
	@cd test/data_amplicon && make all

test_pipeline_x: dummy
	@cd test/data_chrx && make all

test_pipeline_s: dummy
	@cd test/data_somatic && make all

test_pipeline_t: dummy
	@cd test/data_trio && make all

test_pipeline_m: dummy
	@cd test/data_multi && make all

test_pipeline_c: dummy
	@cd test/data_capa && make all

test_pipeline_i: dummy
	@cd test/data_ivac && make all

test_pipeline_e: dummy
	@cd test/data_emed && make all

test_pipeline_r: dummy
	@cd test/data_rna && make all

test_all: dummy
	make test test_tools > t.log 2>&1 &
	make test_pipeline_a > p_a.log 2>&1 &
	make test_pipeline_x > p_x.log 2>&1 &
	make test_pipeline_s > p_s.log 2>&1 &
	make test_pipeline_t > p_t.log 2>&1 &
	make test_pipeline_m > p_m.log 2>&1 &
	make test_pipeline_c > p_c.log 2>&1 &
	make test_pipeline_r > p_r.log 2>&1 &

test_all_status:
	clear && tail -n5 *.log

find_missing_tests: dummy
	php src/Tools/find_missing_tests.php
	
find_unused_tools: dummy
	php src/Tools/find_unused_tools.php -ngsbits ../ngs-bits/ -megsap .

todos:
	find . -name "*.php" | xargs grep "@todo" | egrep -v "somatic|strelka"

swap_settings:
	mv settings.ini settings.ini.swap
	mv settings_nightly.ini settings.ini
	mv settings.ini.swap settings_nightly.ini
	
dummy: