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

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# -----------------------------------------------------------------------
#   Build and install things
# -----------------------------------------------------------------------
.PHONY: build
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build:
	jbuilder build

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.PHONY: install
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install:
	jbuilder install
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.PHONY: build_docker
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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

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.PHONY: push_docker
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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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# -----------------------------------------------------------------------
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#   Tests
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# -----------------------------------------------------------------------
.PHONY: test_simu
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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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.PHONY: test_det
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test_det:
	cd example && \
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	reviewphiltrans detection --outdir outdir/detection --indir outdir/data --preview --np 4 --fast && \
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	mv dag.dot dagtest_det.dot && \
	dot -Tsvg dagtest_det.dot -o dagtest_det.svg
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.PHONY: test_val
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test_val:
	cd example && \
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	reviewphiltrans validation --outdir outdir_validation --tree-dir trees --profile-fn aa_fitness/263SelectedProfiles.tsv --ns 5 --fast --np 4 --seed 4256073781403810077 && \
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	mv dag.dot dagtest_val.dot && \
	dot -Tsvg dagtest_val.dot -o dagtest_val.svg

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# -----------------------------------------------------------------------
#   experiments on real data (only Besnard)
# -----------------------------------------------------------------------
.PHONY: fast_real
fast_real:
	cd example && \
	reviewphiltrans detection --outdir outdir_real_data --indir real_data --fast --np 4 && \
	mv dag.dot dagtest_real.dot && \
	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf

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.PHONY: real
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real:
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	cd example && \
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	reviewphiltrans detection --outdir outdir_real_data --indir real_data --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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# -----------------------------------------------------------------------
#   experiments on threshold choices
# -----------------------------------------------------------------------
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.PHONY: analyses_we
analyses_we:
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	cd example && \
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	reviewphiltrans validation --outdir outdir_analyses_we_0914 --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --seed 2167988076475850536 --fast ; \
	reviewphiltrans validation --outdir outdir_analyses_we_0914 --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --seed 2167988076475850536 ; \
	cp trees4analyses_db/orthomam_* trees_analyses_weekend/ ; \
	reviewphiltrans validation --outdir outdir_analyses_we_0914 --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --seed 2167988076475850536 --fast ; \
	reviewphiltrans validation --outdir outdir_analyses_we_0914 --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --seed 2167988076475850536 ; \
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	mv dag.dot daganalyses_we.dot
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# -----------------------------------------------------------------------
#   Cleaning and formatting
# -----------------------------------------------------------------------
.PHONY: clean
clean:
	rm -rf _build
	rm -rf example/_bistro
	rm -rf example/outdir

.PHONY: clean_test
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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
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.PHONY: format
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format:
	ocp-indent -i lib/*.ml lib/*.mli app/*.ml