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Makefile
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Makefile
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export BIODB_CACHE_DIRECTORY=$(CURDIR)/lcms.biodb.cache
CONDA_PREFIX=$(HOME)/.plncnd
ifndef GALAXY_VERSION
GALAXY_VERSION=18.09
endif
all:
test:
$(MAKE) -C $@
planemo-venv/bin/planemo: planemo-venv
. planemo-venv/bin/activate && pip install "pip>=7"
. planemo-venv/bin/activate && pip install planemo
planemo-venv:
virtualenv planemo-venv
planemolint: planemo-venv/bin/planemo
. planemo-venv/bin/activate && planemo lint --no_xsd
planemotest: R_LIBS_USER=
planemotest: planemo-venv/bin/planemo
. planemo-venv/bin/activate && planemo test --conda_dependency_resolution --conda_prefix "$(CONDA_PREFIX)" --galaxy_branch release_$(GALAXY_VERSION)
planemo-testtoolshed-diff: dist/lcmsmatching/ planemo-venv/bin/planemo
. planemo-venv/bin/activate && cd $< && planemo shed_diff --shed_target testtoolshed
planemo-testtoolshed-update: dist/lcmsmatching/ planemo-venv/bin/planemo
. planemo-venv/bin/activate && cd $< && planemo shed_update --check_diff --shed_target testtoolshed
planemo-toolshed-diff: dist/lcmsmatching/ planemo-venv/bin/planemo
. planemo-venv/bin/activate && cd $< && planemo shed_diff --shed_target toolshed
planemo-toolshed-update: dist/lcmsmatching/ planemo-venv/bin/planemo
. planemo-venv/bin/activate && cd $< && planemo shed_update --check_diff --shed_target toolshed
dist/lcmsmatching/:
mkdir -p $@
cp -r README.md lcmsmatching lcmsmatching.xml test-data $@
clean:
$(MAKE) -C test $@
$(RM) -r $(BIODB_CACHE_DIRECTORY)
$(RM) -r dist
$(RM) -r planemo-venv
$(RM) -r planemotest.log
$(RM) -r $(HOME)/.planemo
$(RM) -r $(CONDA_PREFIX)
$(RM) test_*-output.tsv
$(RM) tool_test_output.*
$(RM) *.zip
.PHONY: all clean test planemo-lint planemo-test planemon-install planemo-toolshed-diff planemo-toolshed-update planemo-testtoolshed-diff planemo-testtoolshed-update pkg