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.travis.yml
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.travis.yml
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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