<commit_before>language: java
sudo: required
dist: trusty
git:
  depth: 9999999
jdk:
- openjdk8
env:
  matrix:
  - TEST_TYPE=cloud
  - TEST_TYPE=integration TEST_VERBOSITY=minimal UPLOAD=true
  - TEST_TYPE=unit TEST_VERBOSITY=minimal
  - TEST_TYPE=integration TEST_DOCKER=true TEST_VERBOSITY=minimal
  - TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
  - RUN_CNV_SOMATIC_WDL=true
  - RUN_M2_WDL=true
  - RUN_CNV_GERMLINE_WDL=true
  global:
  #for genomics db
  - LD_LIBRARY_PATH=$TRAVIS_BUILD_DIR/dependencies/libcsv/.libs
  #gradle needs this
  - TERM=dumb
  #limit gradle jvm memory and disable daemon
  - GRADLE_OPTS="-Xmx1024m -Dorg.gradle.daemon=false"
  #google cloud stuff
  - CLOUDSDK_CORE_DISABLE_PROMPTS=1
  - GCLOUD=$HOME/gcloud/google-cloud-sdk/bin 
  - CLOUDSDK_PYTHON_SITEPACKAGES=1 
  - GOOGLE_APPLICATION_CREDENTIALS=$TRAVIS_BUILD_DIR/servicekey.json
  #Path to GenomicsDB binaries
  - GATK_GENOMICSDB_BIN=src/test/resources/large/tiledb_bin
  #hellbender specific variables
  - HELLBENDER_TEST_INPUTS=gs://hellbender/test/resources/
  - HELLBENDER_TEST_STAGING=gs://hellbender/test/staging/
  - HELLBENDER_TEST_PROJECT=broad-dsde-dev
  - HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=servicekey.json
  #google API key
  - secure: "<KEY>
  #for uploading artifacts
  - ARTIFACTORY_USERNAME=gatkci
  #artifactory password
  - secure: "E0LWXgX3aWSE/DWHXXDx4vrAq4uX6vKg402wToaZ5otbHQ/UP0H7/FA5jomavAXoC46oMVHZcEltZ5OVhuJ0NW8yYxUCecJ1D/YvVQmnfFABcV/qLM+k4e2rYQOKVw/pejB2gG8XdTA+XE2WyTeENbmIkputS8f1ndKWCmZxuuk="
matrix:
  fast_finish: true
  include:
     - jdk: oraclejdk8
       env: TEST_TYPE=integration TEST_VERBOSITY=minimal
before_cache:
  - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
cache:
  directories:
    - $HOME/.gradle/caches/
    - $HOME/.gradle/wrapper/
    - $HOME/gcloud/
before_install:
#setup google stuff
- if [ $TRAVIS_SECURE_ENV_VARS == true ]; then
    openssl aes-256-cbc -K $encrypted_29f3b7c4d8c3_key -iv $encrypted_29f3b7c4d8c3_iv  -in resources_for_CI/servicekey.json.enc -out servicekey.json -d;
    scripts/install_gcloud.sh;
    printf 'y\n' | $GCLOUD/gcloud components update app;
    $GCLOUD/gcloud config set project broad-dsde-dev;
    $GCLOUD/gcloud auth activate-service-account --key-file servicekey.json;
  fi
#install R
- if [[ $TEST_DOCKER != true ]]; then
   sudo mkdir -p /usr/local/lib/R/;
   sudo mkdir -p site-library;
   sudo ln -sFv ~/site-library /usr/local/lib/R/site-library;
   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9;
   sudo add-apt-repository "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/";
   sudo apt-get update;
   sudo apt-get install -y --force-yes r-base-dev=3.1.3-1trusty;
   sudo apt-get install -y --force-yes r-base-core=3.1.3-1trusty;<commit_msg>minor improvements to the .travis.yml (#3101)<commit_after>language: java
sudo: required
dist: trusty
git:
  depth: 9999999
jdk:
- openjdk8
env:
  matrix:
  - TEST_TYPE=cloud
  - TEST_TYPE=integration TEST_VERBOSITY=minimal UPLOAD=true
  - TEST_TYPE=unit TEST_VERBOSITY=minimal
  - TEST_TYPE=integration TEST_DOCKER=true TEST_VERBOSITY=minimal
  - TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
  - RUN_CNV_SOMATIC_WDL=true
  - RUN_M2_WDL=true
  - RUN_CNV_GERMLINE_WDL=true
  global:
  #gradle needs this
  - TERM=dumb
  #limit gradle jvm memory and disable daemon
  - GRADLE_OPTS="-Xmx1024m -Dorg.gradle.daemon=false"
  #google cloud stuff
  - CLOUDSDK_CORE_DISABLE_PROMPTS=1
  - GCLOUD=$HOME/gcloud/google-cloud-sdk/bin 
  - CLOUDSDK_PYTHON_SITEPACKAGES=1 
  - GOOGLE_APPLICATION_CREDENTIALS=$TRAVIS_BUILD_DIR/servicekey.json
  #hellbender specific variables
  - HELLBENDER_TEST_INPUTS=gs://hellbender/test/resources/
  - HELLBENDER_TEST_STAGING=gs://hellbender/test/staging/
  - HELLBENDER_TEST_PROJECT=broad-dsde-dev
  - HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=servicekey.json
  #google API key
  - secure: "<KEY>
  #for uploading artifacts
  - ARTIFACTORY_USERNAME=gatkci
  #artifactory password
  - secure: "E0LWXgX3aWSE/DWHXXDx4vrAq4uX6vKg402wToaZ5otbHQ/UP0H7/FA5jomavAXoC46oMVHZcEltZ5OVhuJ0NW8yYxUCecJ1D/YvVQmnfFABcV/qLM+k4e2rYQOKVw/pejB2gG8XdTA+XE2WyTeENbmIkputS8f1ndKWCmZxuuk="
matrix:
  fast_finish: true
  include:
     - jdk: oraclejdk8
       env: TEST_TYPE=integration TEST_VERBOSITY=minimal
before_cache:
  - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
  - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
cache:
  directories:
    - $HOME/.gradle/caches/
    - $HOME/.gradle/wrapper/
    - $HOME/.m2
    - $HOME/gcloud/
    - $HOME/site-library
before_install:
#setup google stuff
- if [ $TRAVIS_SECURE_ENV_VARS == true ]; then
    openssl aes-256-cbc -K $encrypted_29f3b7c4d8c3_key -iv $encrypted_29f3b7c4d8c3_iv  -in resources_for_CI/servicekey.json.enc -out servicekey.json -d;
    scripts/install_gcloud.sh;
    printf 'y\n' | $GCLOUD/gcloud components update app;
    $GCLOUD/gcloud config set project broad-dsde-dev;
    $GCLOUD/gcloud auth activate-service-account --key-file servicekey.json;
  fi
#install R
- if [[ $TEST_DOCKER != true ]]; then
   sudo mkdir -p /usr/local/lib/R/;
   sudo mkdir -p site-library;
   sudo ln -sFv ~/site-library /usr/local/lib/R/site-library;
   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9;
   sudo add-apt-repository "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/";
   sudo apt-get update;
   sudo apt-get install -y --force-yes r-base-dev=3.1.3-1trusty;
   sudo apt-get install -y --force-yes r-base-core=3.1.3-1trusty;
{'fraction_non_alphanumeric': 0.108604693469165, 'fraction_numerical': 0.027105694014917227, 'mean_word_length': 4.067281105990784, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 2, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2163036', 'n_tokens_mistral': 2442, 'n_tokens_neox': 2302, 'n_words': 358}