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.PHONY: build install build_docker push_docker test clean_test
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build:
	jbuilder build

install:
	jbuilder install
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clean:
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update  
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	rm -r _build || exit 0
	rm -r example/_bistro || exit 0
	rm -r example/outdir || exit 0
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build_docker:
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	@for dir in ./etc/docker/*; \
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	do\
		cd $${dir}; \
		bash ./build_docker.sh; \
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		cd - ; \
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	done

push_docker:
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	@for dir in ./etc/docker/*; \
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	do\
		cd $${dir}; \
		bash ./build_docker.sh push_yes; \
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		cd - ; \
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	done
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test_simu:
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	cd example && \
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	reviewphiltrans pipeline simulation --outdir outdir --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
	mv dag.dot dagtest_sim.dot && \
	dot -Tsvg dagtest_sim.dot -o dagtest_sim.svg
test_det:
	cd example && \
	reviewphiltrans pipeline detection --outdir outdir/detection --indir outdir/data --preview --np 4 && \
	mv dag.dot dagtest_det.dot && \
	dot -Tsvg dagtest_det.dot -o dagtest_det.svg
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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

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