language: python
sudo: false
dist: trusty
python:
  - "3.6"
before_install:
  - cd snakemake/
install:
  - sudo apt-get update
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - conda update -y conda
  - conda config --add channels bioconda
  - conda config --add channels nlesc
  - conda create -y -n wf
  - source activate wf
  - conda install -y snakemake xenon-cli
script:
  - snakemake -C echo_run=1 enable_callers="['manta','delly','lumpy','gridss']"
  - |
    [ $(find data -name *.vcf|wc -l) -eq '12' ] && exit 0 || exit 1;


sudo: true
dist: trusty
language: python
python:
  - "3.6"
services:
  - docker
install:
  - docker pull gtcg/sv-callers-gridengine
  - docker pull gtcg/sv-callers-slurm
  - docker run -d -p 10022:22 --name wf-ge gtcg/sv-callers-gridengine
  - docker run -d -p 10023:22 --name wf-slurm gtcg/sv-callers-slurm
script:
  - |
    sshpass -p javagat ssh -p 10022 xenon@localhost \
      "/bin/bash -l -c '. activate wf;snakemake -v; qinfo"
  - |
    sshpass -p javagat ssh -p 10022 xenon@localhost \
      "/bin/bash -l -c '. activate wf; snakemake -v; sinfo'"
  - |
    [ $(find data -name *.vcf|wc -l) -eq '12' ] && exit 0 || exit 1;

Test workflow in Docker containers.
Test workflow in Docker containers.
