Commit 86a3e08a authored by Estelle Ancelet's avatar Estelle Ancelet
Browse files

add gitlab-ci.yml

parent ad7b1c82
Pipeline #43124 skipped with stages
stages:
- build
- check
- create
- update
image: docker:stable
services:
- docker:dind
variables:
DOCKER_HOST: tcp://docker:2376
DOCKER_TLS_CERTDIR: "/certs"
PLANEMO_IMAGE_TAG: registry.forgemia.inra.fr/record/docker-planemo/docker-planemo-singularity:0.74.1
GALAXY_WRAPPER: siwaa_recipe/galaxy_tools/tools_AZODYN.xml
build azodyn:
stage: build
variables:
IMAGE_TAG: $CI_REGISTRY/$CI_PROJECT_NAMESPACE/azodyn_pea:$CI_COMMIT_SHA
script:
- docker info
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
- docker pull $IMAGE_TAG || true
- docker build --cache-from $IMAGE_TAG -t $IMAGE_TAG -f siwaa_recipe/container/Dockerfile .
- docker push $IMAGE_TAG
when: manual
check azodyn:
stage: check
script:
- docker run $PLANEMO_IMAGE_TAG --version
- head $GALAXY_WRAPPER
- |-
sed -i.bak "s|:latest|:$$CI_COMMIT_SHA</container>|g" $GALAXY_WRAPPER
- head $GALAXY_WRAPPER
- docker run --privileged -v $PWD:/galaxy-central $PLANEMO_IMAGE_TAG lint --report_level error $GALAXY_WRAPPER
- docker run --privileged -v $PWD:/galaxy-central -e SINGULARITY_DOCKER_USERNAME=$SINGULARITY_DOCKER_USERNAME -e SINGULARITY_DOCKER_PASSWORD=$SINGULARITY_DOCKER_PASSWORD $PLANEMO_IMAGE_TAG test --no_cleanup --install_galaxy --galaxy_branch release_21.09 --job_config_file siwaa_recipe/job_conf.xml $GALAXY_WRAPPER
artifacts:
paths:
- tool_test_output.html
- tool_test_output.json
when: always
when: manual
create azodyn:
stage: create
script:
- docker run $PLANEMO_IMAGE_TAG --version
- head $GALAXY_WRAPPER
- |-
sed -i.bak "s|:latest|:$$CI_COMMIT_SHA</container>|g" $GALAXY_WRAPPER
- head $GALAXY_WRAPPER
- docker run --privileged -v $PWD:/galaxy-central $PLANEMO_IMAGE_TAG shed_create --shed_target https://toolshed-siwaa.toulouse.inrae.fr --shed_key $SHED_KEY siwaa_recipe/galaxy_tools
when: manual
# script:
# - planemo --version
# - echo $SHED_EMAIL
# - echo $SHED_PASSWORD
# - planemo shed_create --shed_target "https://toolshed-siwaa.toulouse.inrae.fr/" --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" siwaa_recipe/galaxy_tools
# - planemo shed_create --shed_target https://toolshed-siwaa.toulouse.inrae.fr --shed_email siwaa-support@inrae.fr --shed_password AQJCZw6BZqxrC9P siwaa_recipe/galaxy_tools
# when: manual
update azodyn:
stage: update
script:
- docker run $PLANEMO_IMAGE_TAG --version
- head $GALAXY_WRAPPER
- |-
if [[ $CI_TOOL_TEST_IMAGE != "" ]]; then
sed -i.bak "s|:latest|:$$CI_COMMIT_SHA</container>|g" $GALAXY_WRAPPER
fi
- head $GALAXY_WRAPPER
- docker run --privileged -v $PWD:/galaxy-central $PLANEMO_IMAGE_TAG shed_update --shed_target https://toolshed-siwaa.toulouse.inrae.fr --shed_key $SHED_KEY siwaa_recipe/galaxy_tools
when: manual
......@@ -6,7 +6,7 @@
</plugins>
<destinations>
<destination id="local" runner="local">
<param id="singularity_enabled">true</param>
<param id="singularity_enabled">true</param>
</destination>
</destinations>
</job_conf>
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