Makefile

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

.PHONY: install
install:
	dune install

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

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

# -----------------------------------------------------------------------
#   Test
# -----------------------------------------------------------------------

.PHONY: test
test:
	cd example && \
	reviewphiltrans validation --outdir outdir_test --tree-dir trees_test --profile-fn aa_fitness/263SelectedProfiles.tsv --ns 5  --np 4 --seed 4256073781403810077 && \
	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

# -----------------------------------------------------------------------
#   Test
# -----------------------------------------------------------------------

.PHONY: realdata_test
realdata_test:
	cd example && \
	reviewphiltrans realdata --outdir outdir_realdata_test --indir real_data  --np 4 --seed 4256073781403810077 &&\
	reviewphiltrans realdata --dnds --outdir outdir_realdata_test --indir real_data   --np 4 --seed 4256073781403810077

# -----------------------------------------------------------------------
#   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


# -----------------------------------------------------------------------
#   big experiments
# -----------------------------------------------------------------------
.PHONY: analyses
analyses:
	cd example && \
	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

# -----------------------------------------------------------------------
#   Cleaning and formatting
# -----------------------------------------------------------------------
.PHONY: clean
clean:
	rm -rf _build
	rm -rf example/_bistro
	rm -rf example/outdir

.PHONY: clean-test
clean-test:
	rm -rf example/_bistro
	rm -rf example/outdir_test
	rm -rf example/outdir_realdata_test
	rm -rf example/report.log
	rm -rf example/dot.dag

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