.gitlab-ci.yml

variables:
  PROJECT_NAME: phoenix
stages:
  - build
  - test
  - deploy
before_script:
  - source ~/virtualenvs/$PROJECT_NAME/bin/activate
python-tests:
  stage: test
  script:
    - nosetests --all-modules --with-coverage --cover-html --cover-package=phe test/phe
    - if [ $? -eq 0 ]; then grep pc_cov cover/index.html | egrep -o "[0-9]+\%" | awk '{ print "covered " $1;}' ; else exit 1; fi 
  only:
    - master
end-to-end-tests:
  stage: test
  script:
    - . /etc/profile.d/profile.modules
    - module load uge anaconda/4.0.0 samtools/1.3 bwa/0.7.13 bowtie2 jdk picard-tools gatk
    - PYTHONPATH=.$PYTHONPATH scripts/phenix.py prepare_reference --mapper bwa --variant gatk -r test/scripts/data/reference.fa
    - PYTHONPATH=.$PYTHONPATH scripts/phenix.py prepare_reference --mapper bowtie2 --variant mpileup -r test/scripts/data/reference.fa
    - python test/submit_jobs.py test/scripts/data
    - nosetests --all-modules test/scripts