Makefile

.PHONY: build install build_docker push_docker test clean_test

build:
	jbuilder build

install:
	jbuilder install

clean:
	rm -r _build || exit 0
	rm -r example/_bistro || exit 0
	rm -r example/outdir || exit 0

build_docker:
	@for dir in ./etc/docker/*; \
	do\
		cd $${dir}; \
		bash ./build_docker.sh; \
		cd - ; \
	done

push_docker:
	@for dir in ./etc/docker/*; \
	do\
		cd $${dir}; \
		bash ./build_docker.sh push_yes; \
		cd - ; \
	done

test:
	cd example && \
	reviewphiltrans pipeline --outdir outdir --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
	mv dag.dot dagtest.dot && \
	dot -Tsvg dagtest.dot -o dagtest.svg

test_real:
	cd example && \
	reviewphiltrans pipeline --outdir outdir_real_data --indir real_data --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4
	mv dag.dot dagtest_real.dot && \
	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf

real:
	cd example && \
	reviewphiltrans pipeline --outdir outdir_real_data --indir real_data --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4

analyses_test:
	cd example && \
	reviewphiltrans pipeline --outdir outdir_analyses_test --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --preview  --np 4 && \
	mv dag.dot daganalyses_test.dot && \
	dot -Tpdf  daganalyses_test.dot -o daganalyses_test.pdf

analyses:
	cd example && \
	reviewphiltrans pipeline --outdir outdir_analyses --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 && \
	mv dag.dot daganalyses.dot && \
	dot -Tpdf  daganalyses.dot -o daganalyses.pdf

clean_test:
	rm -r example/_bistro || exit 0
	rm -r example/outdir || exit 0
	rm -r example/report.log || exit 0
	rm -r example/dot.dag || exit 0