buildspec.yml

version: 0.2
run-as: root
env:
  variables:
    "CONTAINER_REPO": "843407916570.dkr.ecr.ap-southeast-2.amazonaws.com"
    "CONTAINER_NAME": "umccrise"
phases:
  install:
    runtime-versions:
      docker: 18
      python: 3.7
  pre_build:
    commands:
      - df -h
      - apt-get update
      - apt-get install -y python3 tree python3-pip git libxt-dev
      - pip3 install --no-cache --upgrade pip
      - pip3 install --no-cache awscli 'dvc[s3]==1.9.1' 'pathspec==0.9.0'
  build:
    commands:
      # Convenience CODEBUILD VARS, need more? Check https://github.com/thii/aws-codebuild-extras
      - export SHORT_COMMIT_HASH=$(echo $CODEBUILD_RESOLVED_SOURCE_VERSION | cut -c 1-10)
      - export UMCCRISE_GIT_TAG="$(git describe --tags --exact-match 2>/dev/null)"
      - if [ -z $UMCCRISE_GIT_TAG ]; then export UMCCRISE_GIT_TAG='NOTAG'; fi
      - export CONTAINER_VERSION=$UMCCRISE_GIT_TAG-$SHORT_COMMIT_HASH
      - echo $CONTAINER_VERSION
      - aws ecr get-login-password | docker login --username AWS --password-stdin 843407916570.dkr.ecr.ap-southeast-2.amazonaws.com
      # Build and tag (-t) image
      - docker build -t $CONTAINER_REPO/$CONTAINER_NAME:$CONTAINER_VERSION .
      - docker images
      - docker system df
      - df -h
  post_build:
    commands:
      # Pull Umccrise reference data
      #- git clone https://github.com/umccr/reference_data reference_data &&
      #  cd reference_data &&
      #  dvc config cache.type reflink,hardlink,copy &&
      #  dvc version &&
      #  dvc remote list &&
      #  dvc pull &&
      #  cd ..
      #- du -sh reference_data/genomes
      #- tree -L 1 reference_data/genomes
      #- df -h
      ## Run minimal test with downsized sample data
      ## Clone sample data repo
      #- git clone --depth 1 https://github.com/umccr/umccrise_test_data umccrise_test_data
      ## Create output directory and set permissions for Docker container user
      #- mkdir -p umccrise_test_data/results/dragen_test_project_docker/ &&
      #  chgrp -R 1000 umccrise_test_data/results/ &&
      #  chmod -R g+w umccrise_test_data/results/
      ## DRAGEN test run
      #- tree -L 1 umccrise_test_data/data/dragen_test_project
      #- docker run -t --cpus 1
      #  -v=$PWD/umccrise_test_data/results/dragen_test_project_docker:/output_dir
      #  -v=$PWD/umccrise_test_data/data/dragen_test_project:/dragen_project
      #  -v=$PWD/reference_data/genomes:/work/genomes
      #  $CONTAINER_REPO/$CONTAINER_NAME:$CONTAINER_VERSION
      #  umccrise /dragen_project -o /output_dir --genomes /work/genomes -j1
      ## Push Docker image to ECR
      #- $(aws ecr get-login --no-include-email --region ap-southeast-2)
      - docker push $CONTAINER_REPO/$CONTAINER_NAME:$CONTAINER_VERSION