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Merge pull request #26 from cancerit/feature/circle-ci
Feature/circle ci
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| version: 2.1 | ||
| jobs: | ||
| build-test-push-job: | ||
| docker: | ||
| - image: circleci/buildpack-deps:stretch | ||
| environment: | ||
| IMAGE_NAME: quay.io/wtsicgp/dockstore-cgpmap | ||
| steps: | ||
| - checkout | ||
| - setup_remote_docker | ||
| - run: | ||
| name: Build Docker image | ||
| command: | | ||
| set -e | ||
| echo "Building Docker image" | ||
| docker build -t test . | ||
| - run: | ||
| name: Validate CWL files | ||
| command: | | ||
| set -e | ||
| echo "Validating CWL files" | ||
| sudo apt-get -y install python3-pip | ||
| pip3 install cwltool | ||
| cwltool --validate Dockstore.cwl | ||
| cwltool --validate cwls/cgpmap-bamBaiOut.cwl | ||
| cwltool --validate cwls/cgpmap-bamCsiOut.cwl | ||
| cwltool --validate cwls/cgpmap-cramOut.cwl | ||
| - run: | ||
| name: Verify inherited programs | ||
| command: | | ||
| set -e | ||
| echo 'Verifying programs inherited from cgpbigwig' | ||
| docker run --rm -t test bwjoin --version | ||
| echo 'Verifying programs inherited from pcap-core' | ||
| docker run --rm -t test bwa_mem.pl -version | ||
| docker run --rm -t test bammarkduplicates2 --version | ||
| docker run --rm -t test samtools --version | ||
| docker run --rm -t test bash -c 'bwa 2>&1 | grep Version' | ||
| - run: | ||
| name: Verify programs | ||
| command: | | ||
| set -e | ||
| echo 'Verify programs from dockstore-cgpmap' | ||
| docker run --rm -t test ds-cgpmap.pl -h | ||
| - run: | ||
| name: Push image to quay.io | ||
| command: | | ||
| set -e | ||
| BRANCH_OR_TAG="${CIRCLE_TAG:-$CIRCLE_BRANCH}" | ||
| if [ "$CIRCLE_TAG" = "$BRANCH_OR_TAG" ]; then | ||
| echo 'Pushing image' | ||
| echo "$DOCKERHUB_PASSWORD" | docker login -u "$DOCKERHUB_USER" --password-stdin | ||
| echo "$QUAYIO_PASSWORD" | docker login -u "$QUAYIO_USER" --password-stdin quay.io | ||
| CLEAN_BRANCH=$(echo $BRANCH_OR_TAG | tr / -) | ||
| docker tag test ${IMAGE_NAME}:${CLEAN_BRANCH} | ||
| docker push ${IMAGE_NAME}:${CLEAN_BRANCH} | ||
| else | ||
| echo "I am not a tag so not pushing image" | ||
| fi | ||
| workflows: | ||
| version: 2.1 | ||
| build-test-push-workflow: | ||
| jobs: | ||
| - build-test-push-job: | ||
| context: | ||
| - dockerhub-casmservice | ||
| - quayio-casmservice | ||
| filters: | ||
| tags: | ||
| only: /.+/ |
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