bulker_config.yaml

bulker:
  volumes: ['$HOME']
  envvars: ['DISPLAY']
  registry_url: http://hub.bulker.io/
  shell_path: ${SHELL}
  shell_rc: ${HOME}/.bashrc
  rcfile: templates/start.sh
  rcfile_strict: templates/start_strict.sh
  default_crate_folder: ${HOME}/bulker_crates
  singularity_image_folder: ${HOME}/simages
  container_engine: docker
  default_namespace: bulker
  executable_template: templates/docker_executable.jinja2
  shell_template: templates/docker_shell.jinja2
  build_template: templates/docker_build.jinja2
  crates:
    waldronlab:
      bioconductor:
        default: ${HOME}/bulker_crates/waldronlab/bioconductor/default
      levi:
        default: ${HOME}/bulker_crates/waldronlab/levi/default
  tool_args:
    waldronlab:
      bioconductor:
        default:
          docker_args: --volume=${HOME}/R/bioc-release:/usr/local/lib/R/host-site-library -e DISABLE_AUTH=true -p 8787:8787 -v ${HOME}:/home/rstudio
        devel:
          docker_args: --volume=${HOME}/R/bioc-devel:/usr/local/lib/R/host-site-library -e DISABLE_AUTH=true -p 8788:8787 -v ${HOME}:/home/rstudio
      curatedmetagenomics:
        default:
          docker_args: --volume=${HOME}/biobakery.db/metaphlan:/usr/local/miniconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases --volume=${HOME}/biobakery.db/humann:/usr/local/humann_databases