142 lines
4.8 KiB
YAML
142 lines
4.8 KiB
YAML
stages:
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- build_and_run
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- release
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image: ${IMAGE}
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variables:
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BASEIMAGE: ${CI_REGISTRY}/${CURRENT_TEMPLATE_IMAGE}
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.install-nextflow: &install-nextflow |
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wget -qO- https://get.nextflow.io | bash
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.install-conda: &install-conda |
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wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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bash Miniconda3-latest-Linux-x86_64.sh -b -p ./miniconda
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source ./miniconda/bin/activate
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conda init
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conda-run:
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image: ubuntu:20.04
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stage: build_and_run
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before_script:
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- apt update && apt install -y wget default-jre
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- *install-nextflow
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- *install-conda
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script:
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- OUTPUT=${CI_PROJECT_NAME}
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- ./nextflow run main.nf
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-w ${OUTPUT}/workspace
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-profile conda
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--fastq test_data/reads.fq.gz
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--out_dir ${OUTPUT}
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only:
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- branches
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build-image:
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stage: build_and_run
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before_script:
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- apk add wget openjdk11 bash
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- *install-nextflow
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script:
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- echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
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- TAG="${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}"
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- docker build --no-cache -t "${TAG}" -f Dockerfile . --build-arg BASEIMAGE=${BASEIMAGE}
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# run letting nextflow orchestrate the containers
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- docker tag "${TAG}" "${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:latest"
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- OUTPUT=${CI_PROJECT_NAME}
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- ./nextflow run main.nf
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-w ${OUTPUT}/workspace
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-profile standard
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--wfversion latest
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--fastq test_data/reads.fq.gz
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--out_dir ${OUTPUT}
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# push
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- if [[ ${CI_COMMIT_BRANCH} == 'dev' ]]; then
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SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA};
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echo "Pushing ${SHATAG}";
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docker tag ${TAG} ${SHATAG};
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docker push ${SHATAG};
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fi;
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only:
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- branches
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artifacts:
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paths:
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# Add the output directory for the test
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- ${CI_PROJECT_NAME}
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expire_in: 1 day
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###
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# Retag the image for git tags (releases)
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.pull_tag: &pull_tag
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before_script:
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- echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
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- SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}
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- echo "Pulling ${SHATAG}"
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- docker pull ${SHATAG}
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only:
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- tags
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# To ONT registry
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release-int:
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stage: release
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<<: *pull_tag
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script:
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- echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
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- RELTAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_NAME}
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- echo "Pushing ${TAG}"
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- docker tag ${SHATAG} ${RELTAG}
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- docker push ${RELTAG}
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# To dockerhub
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release-hub:
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stage: release
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<<: *pull_tag
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script:
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- echo ${DOCKERHUB_TOKEN} | docker login --username epi2melabs --password-stdin
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- RELTAG="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:${CI_COMMIT_TAG}"
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- LATEST="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:latest"
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- echo "Pushing ${RELTAG}"
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- docker tag ${SHATAG} ${RELTAG}
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- docker push ${RELTAG}
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- docker tag ${SHATAG} ${LATEST}
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- docker push ${LATEST}
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# Send all tags matching vX.Y.Z to github (code and release)
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push-github:
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stage: release
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image: $GH_PUSH_IMAGE
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before_script:
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- apt-get update -qq && apt-get install -y -qq
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git python3-all-dev git-lfs python3-venv
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- mkdir ~/.ssh/
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- cp $LABS_BOT_GH_KEY ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
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- echo -e "Host github.com\n\tStrictHostKeyChecking no\n\tHostname ssh.github.com\n\tPort 443\n\n" > ~/.ssh/config
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- git config --global user.email "epi2melabs@nanoporetech.com"
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- git config --global user.name "epi2melabs-bot"
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script:
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# Push master and tag to github
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- git remote add ont ${CI_REPOSITORY_URL} || true
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- git remote add github git@github.com:epi2me-labs/${CI_PROJECT_NAME}.git || true
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- git fetch ont dev --tags
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- git fetch ont master
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- git fetch github master || echo "No 'master' branch present on github"
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- git checkout --track github/master || git checkout master
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- git merge ${CI_COMMIT_TAG}
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- git push github master
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- git push github ${CI_COMMIT_TAG}
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# Make a github release page
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- python3 -m venv release_env --prompt "(release) "
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- source release_env/bin/activate
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- pip install pip --upgrade
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- pip install git+https://github.com/epi2me-labs/github_release.git
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- github_release ${CI_PROJECT_NAME} ${CI_COMMIT_TAG} CHANGELOG.md ${LABS_BOT_GH_TOKEN}
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only:
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- /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/
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except:
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- branches
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