uva_rivanna.yaml

# Environment configuration file for looper
# This version describes the compute environment on Rivanna at UVA
adapters:
  CODE: looper.command
  JOBNAME: looper.job_name
  CORES: compute.cores
  LOGFILE: looper.log_file
  TIME: compute.time
  MEM: compute.mem
  BULKER_CRATE: compute.bulker_crate
  DOCKER_ARGS: compute.docker_args
  DOCKER_IMAGE: compute.docker_image
  SINGULARITY_IMAGE: compute.singularity_image
  SINGULARITY_ARGS: compute.singularity_args
compute_packages:
  default:
    submission_template: templates/slurm_template.sub
    submission_command: sbatch
    partition: standard
  sigterm:
    submission_template: templates/slurm_sig_template.sub
    submission_command: sbatch
    partition: standard
  parallel:
    submission_template: templates/slurm_template.sub
    submission_command: sbatch
    partition: parallel
  largemem:
    submission_template: templates/slurm_template.sub
    submission_command: sbatch
    partition: largemem
  local:
    submission_template: templates/localhost_template.sub
    submission_command: .
  singularity_slurm:
    submission_template: templates/slurm_singularity_template.sub
    submission_command: sbatch
    singularity_args: -B /sfs/lustre:/sfs/lustre,/nm/t1:/nm/t1
  singularity_local:
    submission_template: templates/localhost_singularity_template.sub
    submission_command: .
    singularity_args: -B /apps:/apps
  bulker_slurm:
    submission_template: templates/slurm_bulker_template.sub
    submission_command: sbatch
  bulker_local:
    submission_template: templates/localhost_bulker_template.sub
    submission_command: . 
  
# old idea:
# pipelines: [$CODEBASE/pipelines, $CODEBASE/ATACseq, $CODEBASE/hichip_pipeline, $CODEBASE/open_pipelines]