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:
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	dune build
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.PHONY: install
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install:
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	dune 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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#   Test
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# -----------------------------------------------------------------------
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.PHONY: test
test:
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	cd example && \
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	reviewphiltrans validation --outdir outdir_test --tree-dir trees_test --profile-fn aa_fitness/263SelectedProfiles.tsv --ns 5  --np 4 --seed 4256073781403810077 && \
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	reviewphiltrans validation --outdir outdir_test --tree-dir trees_test --profile-fn aa_fitness/263SelectedProfiles.tsv --dnds --ns 5  --np 4 --seed 4256073781403810077
	#mv dag.dot dagtest_val.dot && \
	#dot -Tsvg dagtest_val.dot -o dagtest_val.svg
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# -----------------------------------------------------------------------
#   Test
# -----------------------------------------------------------------------

.PHONY: realdata_test
realdata_test:
	cd example && \
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	reviewphiltrans realdata --outdir outdir_realdata_test --indir real_data/online_rodent  --np 4 &&\
	reviewphiltrans realdata --pcoc --outdir outdir_realdata_test --indir real_data/online_rodent   --np 4
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# -----------------------------------------------------------------------
#   Realdata
# -----------------------------------------------------------------------

.PHONY: realdata
realdata:
	cd /mnt && \
	mkdir -p wd_reviewphiltrans &&\
	cd wd_reviewphiltrans &&\
	reviewphiltrans realdata --outdir realdata_online_rodents_ensemblkeep --indir /home/ubuntu/data_4_reviewphiltrans_rongeur_ensemblkeep  --np 32 --mem 160 --seed 4256073781403810077
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# -----------------------------------------------------------------------
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#   big experiments
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# -----------------------------------------------------------------------
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.PHONY: analyses
analyses:
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	cd example && \
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	reviewphiltrans validation --outdir outdir_analyses --tree-dir trees_analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --seed 2167988076475850536 ; \
	reviewphiltrans validation --outdir outdir_analyses --tree-dir trees_analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 24 --ns 2000 --seed 2167988076475850536 --diffsel
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# -----------------------------------------------------------------------
#   Cleaning and formatting
# -----------------------------------------------------------------------
.PHONY: clean
clean:
	rm -rf _build
	rm -rf example/_bistro
	rm -rf example/outdir

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.PHONY: clean-test
clean-test:
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	rm -rf example/_bistro
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	rm -rf example/outdir_test
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	rm -rf example/outdir_realdata_test
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	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