.gitlab-ci.yml

---
variables:
  - S3_ENDPOINT: "https://s3.embl.de"
  - S3_BUCKET: "annelids"
stages:
  - upload_to_s3
  - deploy_to_cluster
  - clean_up_on_failure
s3_access_test:
  image: minio/mc
  stage: upload_to_s3
  before_script:
    - mc alias set genomes $S3_ENDPOINT $S3_ACCESS_KEY $S3_SECRET_KEY
  script:
    - mc ls genomes/$S3_BUCKET
cluster_access_test:
  image: dtzar/helm-kubectl:3.8.2
  stage: deploy_to_cluster
  before_script:
    - cd deployment
    - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
    - export KUBECONFIG=/tmp/kubeconf
  script:
    - kubectl config current-context
kustomize_build_apply:
  image: dtzar/helm-kubectl:3.8.2
  stage: deploy_to_cluster
  before_script:
    - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
    - export KUBECONFIG=/tmp/kubeconf
  script:
    - kubectl apply -k deployment
    - kubectl -n $NS wait --for=condition=available --timeout=60s deploy/jbrowse2
  dependencies:
    - cluster_access_test
clean_up_k8s_deployment:
  image: dtzar/helm-kubectl:3.8.2
  stage: clean_up_on_failure
  when: on_failure
  before_script:
    - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
    - export KUBECONFIG=/tmp/kubeconf
  script:
    - echo 'Failed job, deleting resources'
    - kubectl delete -k deployment