.travis.yml

language: python
python:
  # We don't actually use the Travis Python, but this keeps it organized.
  - "3.6"

install:
  - 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:$PATH"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  # Useful for debugging any issues with conda
  - conda info -a
  - conda config --add channels defaults
  - conda config --add channels conda-forge
  - conda config --add channels bioconda
  - sudo apt-get install -y r-base
  - echo 'source("https://bioconductor.org/biocLite.R"); biocLite("S4Vectors"); biocLite("GenomicRanges")' > install.R
  - conda create -q -n snakemake snakemake>=5.1.2 python=$TRAVIS_PYTHON_VERSION star=2.5.3a
  - source activate snakemake
  # create STAR index (too big to live in git)
  - STAR --runMode genomeGenerate --genomeDir .test/resources --genomeFastaFiles .test/resources/GRCh38_chr21.fa
  # moving test data to base directory because this path is hard coded in runGOforDESeq2.R
  - mv .test/home .

script:
  - source activate snakemake
  # run the workflow
  - snakemake --use-conda --directory .test || (for f in .test/logs/*; do echo $f; cat $f; done; for f in .test/logs/*/*; do echo $f; cat $f; done; exit 1)
  - snakemake --use-conda --use-singularity --directory .test