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

sudo: false

services:
  - docker

install:
 - docker build -t dockstore-cgpmap .
 - virtualenv -p python3 venv
 - source venv/bin/activate
 - pip install html5lib cwltool

script:
 - set -e
 - cwltool --validate Dockstore.cwl
 - cwltool --validate cwls/cgpmap-bamOut.cwl
 - cwltool --validate cwls/cgpmap-cramOut.cwl
 - docker images | grep -c dockstore-cgpmap

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
 - cwltool --validate Dockstore.cwl
 - cwltool --validate cwls/cgpmap-bamOut.cwl
 - cwltool --validate cwls/cgpmap-cramOut.cwl
 - docker build -t dockstore-cgpmap .
 - docker images | grep -c dockstore-cgpmap
 - docker run -ti --rm dockstore-cgpmap ds-cgpmap.pl -h
 - docker run -ti --rm dockstore-cgpmap bwa_mem.pl -version
 - docker run -ti --rm dockstore-cgpmap bammarkduplicates2 --version
 - docker run -ti --rm dockstore-cgpmap samtools --version
 - docker run -ti --rm dockstore-cgpmap bash -c 'bwa 2>&1 | grep Version'

Test commands expected are available
Test commands expected are available
