MOSuite-Galaxy

Galaxy workflow configuration for MOSuite

MOSuite Workflow on Galaxy: http://k8s-galaxy-b671dd4f69-710212292.us-east-1.elb.amazonaws.com/u/kelly-sovacool/w/mosuite

Updating the Galaxy XML files for MOSuite

Installation

pip install git+https://github.com/CCBR/MOSuite-Galaxy

Usage

galaxysynth --help

usage: galaxysynth [-h] [-o OUTPUT] [--docker DOCKER] [--citation CITATION]
                   [--repo-name REPO_NAME] [--cli-command CLI_COMMAND]
                   [--pkg-name PKG_NAME] [--debug] [-v]
                   blueprint

Generate Galaxy tool XML from blueprint JSON files with sanitizer and section
support

positional arguments:
  blueprint             Path to blueprint JSON file or pattern (e.g.,
                        'templates/3_galaxy-tools/*.json')

options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Output directory for XML files (default: galaxy_tools)
  --docker DOCKER       Docker image name (default: nciccbr/mosuite:latest)
  --citation CITATION   Citation DOI (default: 10.5281/zenodo.16371580)
  --repo-name REPO_NAME
                        Repository name used for references (default:
                        CCBR/MOSuite-Galaxy)
  --cli-command CLI_COMMAND
                        CLI command to invoke templates (default: mosuite)
  --pkg-name PKG_NAME   R package name for documentation links (default:
                        MOSuite)
  --debug               Enable debug output
  -v, --version         show program's version number and exit

galaxysynth  "templates/2_blueprints/*.json" \
    --docker nciccbr/mosuite:v0.3.0 \
    --output templates/3_galaxy-tools

Developer notes

• Please view the contributing guide before opening a pull request.
• Galaxy Tool XML documentation: https://docs.galaxyproject.org/en/master/dev/schema.html