.travis.yml

sudo: required

services:
  - docker

env:
  TAG=$(git describe --long --always --tags)
  PATH=/snap/bin:$PATH

before_install:
  - sudo apt-get update && sudo apt-get install --only-upgrade openssl
  - sudo pip install --user urllib3[secure] --upgrade
  - tar -czf resources.tar.gz resources/
  - docker build -t dnanexus/parliament2:$TAG .
  - sudo bash test/set_up_tests.sh

jobs:
  include:
    - stage: testing
      script: docker run dnanexus/parliament2:$TAG -q -h
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix breakdancer --breakdancer && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix breakseq --breakseq && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --prefix cnvnator --cnvnator && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --ref_genome /home/dnanexus/in/ref.fa.gz --prefix delly_deletion --delly_deletion && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix delly_duplication --delly_duplication && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix delly_insertion --delly_insertion && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix delly_inversion --delly_inversion && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix lumpy --lumpy && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix manta --manta && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix svviz --breakdancer --svviz && ls -sh /home/dnanexus/out
    - script: docker run -v /home/dnanexus/in:/home/dnanexus/in -v /home/dnanexus/out:/home/dnanexus/out dnanexus/parliament2:$TAG --bam /home/dnanexus/in/small_input.bam --bai /home/dnanexus/in/small_input.bai --ref_genome /home/dnanexus/in/ref.fa.gz --fai /home/dnanexus/in/ref.fa.fai --prefix full --breakdancer --genotype && ls -sh /home/dnanexus/out


deploy:
  provider: script
  script: echo "$DOCKER_PASSWORD" | docker login --username "$DOCKER_USERNAME" --password-stdin && docker push dnanexus/parliament2:$TAG
  on:
    branch: master

branches:
  except:
  - hgsc

language: python
python: 
  - "2.7.13"