.travis.yml

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

sudo: false

language: ruby

services:
  - docker

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

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