Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

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.PHONY: build install clean build_docker push_docker clean_test test_simu test_det test_val real analyses_30Bloom analyses_263Bloom
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build:
	jbuilder build

install:
	jbuilder install
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clean:
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	rm -rf _build
	rm -rf example/_bistro
	rm -rf example/outdir
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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 simulation --outdir outdir --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
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	mv dag.dot dagtest_sim.dot && \
	dot -Tsvg dagtest_sim.dot -o dagtest_sim.svg
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test_det:
	cd example && \
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	reviewphiltrans detection --outdir outdir/detection --indir outdir/data --preview --np 4 && \
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	mv dag.dot dagtest_det.dot && \
	dot -Tsvg dagtest_det.dot -o dagtest_det.svg
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test_val:
	cd example && \
	reviewphiltrans validation --outdir outdir_validation --indir real_data --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
	mv dag.dot dagtest_val.dot && \
	dot -Tsvg dagtest_val.dot -o dagtest_val.svg

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real:
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	cd example && \
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	reviewphiltrans detection --outdir outdir_real_data --indir real_data --preview --np 4 && \
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	mv dag.dot dagtest_real.dot && \
	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf

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analyses_30Bloom:
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	cd example && \
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	reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30 --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 && \
	mv dag.dot daganalyses_tiragesBloomK30.dot
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analyses_263Bloom:
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	cd example && \
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	reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 && \
	mv dag.dot daganalyses_263SelectedProfiles.dot
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clean_test:
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	rm -rf example/_bistro
	rm -rf example/outdir
	rm -rf example/report.log
	rm -rf example/dot.dag