.travis.yml

dist: bionic

cache:
  directories:
    - /home/travis/build/BodenmillerGroup/ImcSegmentationSnakemake/.snakemake/singularity
language: python
python:
  # We don't actually use the Travis Python, but this keeps it organized.
  - "3.8"

install:
  - sudo apt-get update
  - sudo apt-get install singularity-container
  - 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
  - conda install -q -c conda-forge mamba
  - mamba create -q -n snakemake bioconda::snakemake

script:
  - source activate snakemake
  # run the workflow
  - snakemake resources/example_data --use-conda --use-singularity --cores 2 --config ilastik_mem_mb=4000
  - snakemake --use-conda --use-singularity --cores 2 --config ilastik_mem_mb=4000