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Makefile
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app_name = metaMS
parameters_path = data/MetamsFile.json
# change the path to your data path and configuration
data_dir = /Users/eber373/Development/metams/data
config_dir = /Users/eber373/Development/metams/configuration
version := $(shell cat .bumpversion.cfg | grep current_version | cut -d= -f2 | tr -d ' ')
stage := $(shell cat .bumpversion.cfg | grep optional_value | cut -d= -f2 | tr -d ' ')
cpu:
pyprof2calltree -k -i $(file)
mem:
mprof run --multiprocess $(script)
mprof plot
major:
@bumpversion major --allow-dirty
@make bump_lipid_major
@make convert_lipid_rst_to_md
minor:
@bumpversion minor --allow-dirty
@make bump_lipid_minor
@make convert_lipid_rst_to_md
patch:
@bumpversion patch --allow-dirty
@make bump_lipid_patch
@make convert_lipid_rst_to_md
bump_lipid_major:
@bumpversion major --allow-dirty --config-file .bumpversion_lipid.cfg
bump_lipid_minor:
@bumpversion minor --allow-dirty --config-file .bumpversion_lipid.cfg
bump_lipid_patch:
@bumpversion patch --allow-dirty --config-file .bumpversion_lipid.cfg
install:
@source venv/bin/activate
@pip3 install --editable .
run:
@ . venv/bin/activate
@metaMS run-gcms-workflow $(parameters_path)
pypi:
@python3 setup.py sdist
@twine upload dist/*
docker-push:
@echo corilo/metams:$(version)
@docker build --no-cache -t corilo/metams:$(version) .
@docker push corilo/metams:$(version)
@docker image tag corilo/metams:$(version) corilo/metams:latest
@docker push corilo/metams:latest
docker-push-heal:
@echo katherineheal257/metams:$(version)
@docker buildx create --use
@docker buildx build --platform linux/amd64,linux/arm64 --no-cache -t katherineheal257/metams:$(version) --push .
@docker buildx imagetools create katherineheal257/metams:$(version) -t katherineheal257/metams:latest
@docker buildx imagetools inspect katherineheal257/metams:latest
docker-nmdc:
@echo microbiomedata/metams:$(version)
@docker buildx create --use
@docker buildx build --platform linux/amd64,linux/arm64 --no-cache -t microbiomedata/metams:$(version) --push .
@docker buildx imagetools create microbiomedata/metams:$(version) -t microbiomedata/metams:latest
@docker buildx imagetools inspect microbiomedata/metams:latest
echo-version:
@echo $(version)
docker-build:
docker build -t microbiomedata/metams:latest .
docker-build-local:
docker build -t local-metams:latest .
docker-run:
@echo $(data_dir)
@echo $(config_dir)
@docker run -v $(data_dir):/metams/data -v $(config_dir):/metams/configuration microbiomedata/metams:latest metaMS run-gcms-workflow /metams/configuration/metams.toml
wdl-run-gcms :
@miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files
wdl-run-gcms-local:
@make docker-build-local
@miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms_local_docker.json --verbose --no-cache --copy-input-files
wdl-run-lipid :
miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files
convert_lipid_rst_to_md:
# convert the lipid documentation from rst to md
pandoc -f rst -t markdown -o docs/lcms_lipidomics/README_LCMS_LIPID.md docs/lcms_lipidomics/index.rst
# render the lipid documentation into html from the rst file
pandoc -f rst -t html -o docs/lcms_lipidomics/index.html docs/lcms_lipidomics/index.rst