How to use looper with bulker

Bulker is a multi-container environment manager that provides containerized CLI tools via lightweight shim scripts. Looper ships with built-in compute packages for running bulker-activated pipelines, both locally and on SLURM clusters.

1. Specify the bulker crate in your pipeline interface

The pipeline author specifies which bulker crate to use in the compute section of the pipeline interface:

pipeline_name: my_pipeline
sample_interface:
  command_template: >
    my_tool {sample.input_file}
compute:
  bulker_crate: bulker/demo:default

2. Run locally with bulker_local

To run bulker-activated pipelines on your local machine:

looper run --package bulker_local

This activates the bulker crate and runs the pipeline command inside the bulker environment. The submission command is sh, so jobs run sequentially in the current shell.

3. Submit to SLURM with bulker_slurm

To submit bulker-activated pipelines to a SLURM cluster:

looper run --package bulker_slurm \
  --compute partition=standard time='04:00:00' cores='8' mem='16000'

This uses the built-in bulker_slurm template, which handles SLURM submission headers and bulker activation automatically.

4. Use pre-commands for environment setup

On many HPC systems, bulker needs additional setup before it can run — for example, loading a module or setting TMPDIR to a shared scratch location. Use pre_command for this:

looper run --package bulker_slurm \
  --compute partition=standard time='04:00:00' cores='8' mem='16000' \
  pre_command='export TMPDIR=/scratch/$USER/tmp && mkdir -p $TMPDIR && module load apptainer'

Or set it in your looper config so you don't have to type it every time:

pep_config: pep_config.yaml
output_dir: results
pipeline_interfaces:
  - pipeline/pipeline_interface.yaml
cli:
  run:
    package: bulker_slurm
    compute:
      partition: standard
      time: '04:00:00'
      cores: '8'
      mem: '16000'
      pre_command: >
        export TMPDIR=/scratch/$USER/tmp && mkdir -p $TMPDIR && module load apptainer

Available bulker packages

Package	Submission	Description
`bulker_local`	`sh`	Run bulker-activated pipelines locally
`bulker_slurm`	`sbatch`	Submit bulker-activated pipelines to SLURM

Appendix: Built-in bulker templates

bulker_local template

#!/bin/bash

echo 'Compute node:' `hostname`
echo 'Start time:' `date +'%Y-%m-%d %T'`

{PRE_COMMAND}

eval "$(bulker activate -e {BULKER_CRATE})"

{
  {CODE}
} | tee {LOGFILE} -i

{POST_COMMAND}

bulker_slurm template

#!/bin/bash
#SBATCH --job-name='{JOBNAME}'
#SBATCH --output='{LOGFILE}'
#SBATCH --mem='{MEM}'
#SBATCH --cpus-per-task='{CORES}'
#SBATCH --time='{TIME}'
#SBATCH --partition='{PARTITION}'
#SBATCH -m block
#SBATCH --ntasks=1

echo 'Compute node:' `hostname`
echo 'Start time:' `date +'%Y-%m-%d %T'`

{PRE_COMMAND}

eval "$(bulker activate -e {BULKER_CRATE})"

{CODE}

{POST_COMMAND}