.travis.yml

notifications:
  slack: wtsi-cgpit:ptUMR1tkNyZJYd9TpGoss8WR
  email: false

sudo: false

services:
  - docker

install:
 - virtualenv -p python3 venv
 - source venv/bin/activate
 - pip install html5lib cwltool

script:
 - set -e
 - echo 'Validate CWL file(s)'
 - cwltool --validate cwls/cgpwgs.cwl
 - echo 'Build and check docker image'
 - docker build -t dockstore-cgpwgs .
 - docker images | grep -c dockstore-cgpwgs
 - echo 'Verify program from each inherited package is found (dockstore-cgpbigwig)'
 - docker run -t --rm dockstore-cgpwgs bwjoin --version
 - echo 'Verify program from each inherited package is found (dockstore-cgpmap)'
 - docker run -t --rm dockstore-cgpwgs ds-cgpmap.pl -h
 - docker run -t --rm dockstore-cgpwgs bwa_mem.pl -version
 - docker run -t --rm dockstore-cgpwgs bammarkduplicates2 --version
 - docker run -t --rm dockstore-cgpwgs samtools --version
 - docker run -t --rm dockstore-cgpwgs bash -c 'bwa 2>&1 | grep Version'
 - echo 'Verify program from each inherited package is found (dockstore-cgpwxs)'
 - docker run -t --rm dockstore-cgpwgs ds-cgpwxs.pl -h
 - docker run -t --rm dockstore-cgpwgs cgpVCFSplit.pl -version
 - docker run -t --rm dockstore-cgpwgs vcftools --version
 - docker run -t --rm dockstore-cgpwgs bedtools --version
 - docker run -t --rm dockstore-cgpwgs bash -c 'pindel 2>&1 | grep Welcome'
 - docker run -t --rm dockstore-cgpwgs pindel.pl -version
 - docker run -t --rm dockstore-cgpwgs caveman --version
 - docker run -t --rm dockstore-cgpwgs caveman.pl -version
 - docker run -t --rm dockstore-cgpwgs cgpFlagCaVEMan.pl -version
 - docker run -t --rm dockstore-cgpwgs AnnotateVcf.pl -version
 - echo 'Verify a program from each new package is found (dockstore-cgpwgs)'
 - docker run -t --rm dockstore-cgpwgs ds-cgpwgs.pl -h
 - docker run -t --rm dockstore-cgpwgs bash -c 'verifyBamID 2>&1 | grep verifyBamID'
 - docker run -t --rm dockstore-cgpwgs alleleCounter --version
 - docker run -t --rm dockstore-cgpwgs brass.pl -version
 - docker run -t --rm dockstore-cgpwgs ascat.pl -version