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.gitlab-ci.yml
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.gitlab-ci.yml
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image: "pfem/planemo"
# stages
stages:
- build-docker
# - perl-unit-test
- planemo-pre-run
- planemo-test
# - release-ts-pfem
# - release-ts-test
- release-ts-prod
variables:
DOCKER_IMAGE: "pfem/planemo"
TS_PFEM_TARGET: "https://unh-toolshedpfem.ara.inrae.fr/"
TS_MAIN_TARGET: "toolshed"
TS_TEST_TARGET: "testtoolshed"
build docker:
stage: build-docker
tags:
- shell
script:
- docker build -t $DOCKER_IMAGE .
#perl-unit-test:
# stage: perl-unit-test
# script:
# - prove -l t
# - ls -R
# tags:
# - docker
planemo-lint:
stage: planemo-pre-run
script:
- echo "==================================";
- echo "[info] lint tool with planemo ";
- . "$PLANEMO_VENV_LOCATION"/bin/activate ;
- planemo lint --fail_level error ./*.xml
tags:
- docker
planemo-test:
stage: planemo-test
script:
- echo "==================================";
- echo "[info] Testing tool locally without planemo for this version ";
# - . "$PLANEMO_VENV_LOCATION"/bin/activate ;
# - planemo conda_install --conda_prefix=/tmp/mc .
# - planemo test --conda_dependency_resolution --conda_prefix /tmp/mc/ --install_galaxy --galaxy_python_version 3.8 --galaxy_single_user --test_data ./test-data ./*.xml
# - planemo test --conda_auto_init --galaxy_python_version 3.8 --test_data ./test-data ./*.xml
# - planemo test --no_dependency_resolution --galaxy_root=/tmp/galaxy --no_conda_auto_init --galaxy_source https://github.com/galaxyproject/galaxy --galaxy_branch release_23.1 --galaxy_python_version 3.8 --test_timeout 900 --test_data ./test-data ./*.xml
tags:
- docker
# release-toolshed-pfem:
# stage: release-ts-pfem
# tags:
# - docker
# script:
# - echo "==================================";
# - echo "[info] Upload tool on pfem-ts with planemo ";
# - . "$PLANEMO_VENV_LOCATION"/bin/activate ;
# - echo "planemo shed_update --shed_key=$TS_PFEM_KEY --check_diff --shed_target $TS_PFEM_TARGET"
# - planemo shed_update --shed_key=$TS_PFEM_KEY --check_diff --shed_target $TS_PFEM_TARGET--message=" Dev branch Updating - - Fxx"
# except:
# refs:
# - master
# - tags
# release-toolshed-test:
# stage: release-ts-test
# tags:
# - docker
# script:
# - echo "==================================";
# - echo "[info] Upload tool on test-ts with planemo ";
# - . "$PLANEMO_VENV_LOCATION"/bin/activate ;
# - echo "planemo shed_update --shed_key=$TS_TEST_KEY --check_diff --shed_target $TS_TEST_TARGET"
# - planemo shed_update --shed_key=$TS_TEST_KEY --check_diff --shed_target $TS_TEST_TARGET --message=" master branch Updating - - Fxx"
# only:
# refs:
# - master
release-toolshed-prod:
stage: release-ts-prod
tags:
- docker
script:
- echo "==================================";
- echo "[info] Upload tool on main-ts planemo ";
- . "$PLANEMO_VENV_LOCATION"/bin/activate ;
- echo "planemo shed_update --shed_key=$TS_MAIN_KEY --check_diff --shed_target $TS_MAIN_TARGET"
- planemo shed_update --shed_key=$TS_MAIN_KEY --check_diff --shed_target $TS_MAIN_TARGET --message=" master branch Updating with tag $env:CI_COMMIT_TAG - - Fxx"
only:
refs:
- tags