.travis.yml

sudo: required
services:
- docker

language: java
jdk:
- oraclejdk8


# found at https://github.com/GoogleCloudPlatform/Template/blob/master/.travis.yml
cache:
  directories:
      - $HOME/gcloud/

env:
    global:
    # These environment variables are set up for all the parallel jobs to use
      - PATH=$PATH:$HOME/gcloud/google-cloud-sdk/bin GOOGLE_APPLICATION_CREDENTIALS=$TRAVIS_BUILD_DIR/client_secrets.json #Other environment variables on same line
      - wget https://github.com/broadinstitute/cromwell/releases/download/34/cromwell-34.jar  --directory-prefix=$TRAVIS_BUILD_DIR/tests
    matrix:
       # These environment variables specify that these tests will run in parallel
       # We need to do this because the aligner and variant caller pipelines take
       # a relatively long time to execute
       - TEST_SUITE=test_CRAM_to_md5sum_checker.sh
#      - TEST_SUITE=test_aligner_WDL_checker.sh
#      - TEST_SUITE=test_aligner_CWL_checker.sh
#      - TEST_SUITE=test_variant_caller_WDL_checker.sh
#      - TEST_SUITE=test_variant_caller_CWL_checker.sh

before_install:
        #ENCRYPT YOUR PRIVATE KEY (If you need authentication)
        # 1. Install and login to the Travis CLI:
        #       $ gem install travis
        #       $ travis login
        # 2. Move your json private key to client_secrets.json
        # 3. Run:
        #       $ travis encrypt-file client_secrets.json --add
        # 4. Commit changes:
        #       $ git add client_secrets.json.enc
        #       $ git commit client_secrets.json.enc .travis.yml

        - if [ ! -d $HOME/gcloud/google-cloud-sdk ]; then
                mkdir -p $HOME/gcloud &&
                wget https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz --directory-prefix=$HOME/gcloud &&
                cd $HOME/gcloud &&
                tar xzf google-cloud-sdk.tar.gz &&
                printf '\ny\n\ny\ny\n' | ./google-cloud-sdk/install.sh &&
                cd $TRAVIS_BUILD_DIR;
          fi
          #        - gcloud -q components update

        - if [ -a client_secrets.json ]; then
                gcloud -q auth activate-service-account --key-file client_secrets.json;
          fi


install:
- docker version

- pip2.7 install --user setuptools==36.5.0
- pip2.7 install --user cwl-runner cwltool==1.0.20170828135420 schema-salad==2.6.20170806163416 avro==1.8.1 ruamel.yaml==0.14.12 requests==2.18.4

   # Install crcmod for faster gsutil downloads
   # https://cloud.google.com/storage/docs/gsutil/addlhelp/CRC32CandInstallingcrcmod
-  sudo -H apt-get install gcc python-dev python-setuptools
-  sudo -H easy_install -U pip
  #-  sudo -H pip uninstall crcmod
-  sudo -H pip install -U crcmod

script:
# Execute each line separately using the literal style block scalar for yaml
# http://yaml.org/spec/1.2/spec.html#id2795688
 - |
   cwltool --version
   java -version
   java -jar cromwell-34.jar --version
   gsutil --version

   pwd
   ls -al
   df -h
   sudo du -hsx ./* | sort -n | head -100
   java -XX:+PrintCommandLineFlags


   cd $TRAVIS_BUILD_DIR/tests/

   pwd
   ls -al

   # Have Travis CI wait for a set time even if the workflows do not provide output
   # for 30 seconds
   travis_wait 55 ./$TEST_SUITE