puma.yaml

# Environment configuration file for looper
# This version describes the compute environment on Rivanna at UVA

compute_packages:
  default:
    submission_template: templates/localhost_template.sub
    submission_command: sh
  local:
    submission_template: templates/localhost_template.sub
    submission_command: sh
  default:
    submission_template: templates/localhost_template.sub
    submission_command: sh
  singularity:
    submission_template: templates/localhost_singularity_template.sub
    submission_command: sh
    singularity_args: -B /ext:/ext
  bulker_local:
    submission_template: templates/localhost_bulker_template.sub
    submission_command: sh    
  docker:
    submission_template: templates/localhost_docker_template.sub
    submission_command: sh
    docker_args: |
      --user=$(id -u):$(id -g) \
      --env="DISPLAY" \
      -e "GENOMES" \
      -e "REFGENIE" \
      --volume="$EXTDATA:$EXTDATA" \
      --volume="/project:/project" \
      --volume ${CODEBASE}:${CODEBASE} \
      --volume ${PROCESSED}:${PROCESSED} \
      --volume="/etc/group:/etc/group:ro" \
      --volume="/etc/passwd:/etc/passwd:ro" \
      --volume="/etc/shadow:/etc/shadow:ro"  \
      --volume="/etc/sudoers.d:/etc/sudoers.d:ro" \
      --volume="/tmp/.X11-unix:/tmp/.X11-unix:rw" \
      --workdir="`pwd`" \

# old idea:
# pipelines: [$CODEBASE/pipelines, $CODEBASE/ATACseq, $CODEBASE/hichip_pipeline, $CODEBASE/open_pipelines]