.travis.yml

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

sudo: false

services:
  - docker

script:
 - set -e
 - echo 'Build and check docker image'
 - docker build -t cgprna .
 - docker images | grep -c cgprna
 - echo 'Verify program(s) from each inherited base image - dockstore-cgpbigwig'
 - docker run -t --rm cgprna bwjoin --version
 - echo 'Verify program(s) from each inherited base image - dockstore-cgpmap'
 - docker run -t --rm cgprna bwa_mem.pl -version
 - docker run -t --rm cgprna bammarkduplicates2 --version
 - docker run -t --rm cgprna samtools --version
 - docker run -t --rm cgprna bash -c 'bwa 2>&1 | grep Version'
 - echo 'Verify program(s) from this repo'
 ## mapping
 - docker run -t --rm cgprna star_mapping.pl --version
 ## RSeQC
 - docker run -t --rm cgprna split_bam.py --version
 - docker run -t --rm cgprna geneBody_coverage.py --version
 - docker run -t --rm cgprna read_distribution.py --version
 ## BAM QC
 - docker run -t --rm cgprna process_qcstats.pl --version
 ## count
 - docker run -t --rm cgprna which htseq-count
 ## fusion
 - docker run -t --rm cgprna tophat_fusion.pl --version
 - docker run -t --rm cgprna star_fusion.pl --version
 - docker run -t --rm cgprna defuse_fusion.pl --version
 - docker run -t --rm cgprna which compare_overlapping_fusions.pl
 ## some dependencies used by more than one tool
 - docker run -t --rm cgprna bedtools --version
 - docker run -t --rm cgprna R --version
 - docker run -t --rm cgprna which blat
 ### tophat dependencies
 - docker run -t --rm cgprna bowtie --version
 - docker run -t --rm cgprna bowtie2 --version
 ### tophat-fusion dependencies
 - docker run -t --rm cgprna blastn -version
 ### Defuse dependencies
 - docker run -t --rm cgprna which faToTwoBit
 - docker run -t --rm cgprna gmap --version