dekupl-annotation/.gitlab-ci.yml at master · Transipedia/dekupl-annotation · GitHub

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docker_base:
  image: docker:stable
  stage: build
  services:
    - docker:dind
  before_script:
    - echo "$CI_JOB_TOKEN" | docker login -u gitlab-ci-token --password-stdin "$CI_REGISTRY"
  script:
    - docker pull "$CI_REGISTRY_IMAGE":base || true
    - docker build --cache-from "$CI_REGISTRY_IMAGE":base -t "$CI_REGISTRY_IMAGE":base -f Dockerfile.base .
    - docker push "$CI_REGISTRY_IMAGE":base
  only:
    changes:
      - Dockerfile.base
      - install_r_packages.R

test:
  image: registry.gitlab.com/transipedia/dekupl-annotation:base
  stage: test
  before_script:
    # Install dkpl-annot with Dist-zilla and CPAN-minus
    - dzil install --install-command 'cpanm .'
  script:
    - dkpl index -g toy/references/GRCh38-chr22.fa.gz -a toy/references/GRCh38-chr22.gff.gz -i test_index
    - dkpl annot -v -i test_index --deg toy/dkpl-run/DEGs.tsv.gz toy/dkpl-run/merged-diff-counts.tsv.gz
    - dkpl annot -v -i test_index --deg toy/dkpl-run/DEGs.tsv.gz --norm-gene-counts toy/dkpl-run/normalized_counts.tsv --sample-conditions toy/dkpl-run/sample_conditions_full.tsv toy/dkpl-run/merged-diff-counts.tsv.gz
    - dkpl index -g toy/references/GRCh38-chr22.fa.gz -a toy/references/GRCh38-chr22.gff.gz -i test_index_star --star
    - dkpl annot -v -i test_index_star --deg toy/dkpl-run/DEGs.tsv.gz toy/dkpl-run/merged-diff-counts.tsv.gz -o test_STAR

delivery-conda:
  image: continuumio/miniconda3:4.5.11
  stage: deploy
  only:
    - tags
  script:
    - apt-get update -q -y
    - apt-get install -y build-essential cpanminus libdist-zilla-perl
    - conda config --set always_yes yes --set changeps1 no
    - conda config --add default_channels https://repo.anaconda.com/pkgs/pro
    - conda config --add default_channels https://repo.anaconda.com/pkgs/free
    - conda config --add default_channels https://repo.anaconda.com/pkgs/main
    - conda config --add channels conda-forge
    - conda config --add channels defaults
    - conda config --add channels bioconda
    - conda create -n build anaconda-client conda-build
    - source activate build
    - conda info -a
    - dzil build --in build
    - conda build --user transipedia --token $ANACONDA_TOKEN recipe

delivery-docker:
  image: docker:latest
  services:
    - docker:dind
  stage: deploy
  only:
    - tags
  script:
    - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
    - docker build --pull -t transipedia/dekupl-annotation -t transipedia/dekupl-annotation:$CI_COMMIT_REF_NAME .
    - docker push transipedia/dekupl-annotation