Overview

Module and script for bootstrapping Galaxy job config files.

• Code: https://github.com/galaxyproject/galaxy-job-config-init

Installation

Install from PyPI:

pip install galaxy-job-config-init

CLI Usage

The package provides two command-line tools:

galaxy-job-config-init

Generate job configuration YAML for Galaxy:

galaxy-job-config-init [OPTIONS]

Options:

--galaxy-version TEXT
    Generate job config YAML for this version of Galaxy

--runner {local,slurm,pbs,condor,kubernetes}
    Galaxy runner (e.g. DRM) to target (defaults to 'local')

--tpv
    Enable shared TPV database

--docker
    Enable Docker

--docker-cmd TEXT
    Command used to launch docker (defaults to 'docker')

--docker-host TEXT
    Docker host

--docker-sudo
    Use sudo with Docker

--docker-sudo-cmd TEXT
    Docker sudo command

--docker-run-extra-arguments TEXT
    Extra arguments for Docker run

--docker-extra-volume TEXT
    Extra Docker volumes (can be specified multiple times)

--singularity
    Enable Singularity

--singularity-cmd TEXT
    Command used to execute singularity (defaults to 'singularity')

--singularity-sudo
    Use sudo with Singularity

--singularity-sudo-cmd TEXT
    Singularity sudo command

--singularity-extra-volume TEXT
    Extra Singularity volumes (can be specified multiple times)

--tmp-dir TEXT
    Configure temporary directory handling (defaults to 'true')

--all-in-one-handling
    Use all-in-one job handling configuration

galaxy-job-config-init-summary

Generate a summary of the job configuration. See job_config_examples.md for detailed examples of generated configurations.

Examples

Generate a basic local job configuration:

galaxy-job-config-init

Generate configuration for SLURM with Docker support:

galaxy-job-config-init --runner slurm --docker

Generate configuration with custom Docker volumes:

galaxy-job-config-init --docker --docker-extra-volume /data:/data --docker-extra-volume /scratch:/scratch

Generate configuration for all-in-one Galaxy instance:

galaxy-job-config-init --all-in-one-handling

Contributing

Contributions are welcome! Please see CONTRIBUTING.rst for development setup, code quality guidelines, and release procedures.