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usegalaxy.* tools

Originally this repository was solely for the use of usegalaxy.eu, but we are looking at expanding that to the other usegalaxy.* instances. Some documentation may be outdated while we figure out the new policies and procedures.

Currently only UseGalaxy.eu is installing tools from this repository.

Best used with ...

ephemeris. Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows.

You can use ephemeris with our tool defintions as easy as:

shed-tools install -t tools_iuc.yaml -g https://mygalaxy.xy -a API-KEY

Setup

  • yaml files are manually curated
  • yaml.lock files are automatically generated
  • Only IUC tools are automatically updated with the latest version each week

Requesting Tools in UseGalaxy.*

Policies are not set in stone and we would be happy to seek feedback and discussions. Currenty, we encourage everyone to submit tools via PRs to this repo. The tools are losely grouped into several categories based on the yaml files. Please make your changes in the appropriate file and avoid creating a new yaml file unless necessary.

However, we promise a high-quality service to our users and we need to ensure sustainability of the installed tools. That means that tools are regularly updated, tested and can be adjusted to new developments. Therefore, we encourage everyone to follow the IUC Guidelines for tool development and have automatic testing enabled via CI.

We encourage you to submit your tool to one of the larger community repositories, like

These repositories have planemo CI testing enabled and have a larger communities in place that help you with maintaining the tools.

Updating an Existing Tool

  • Edit the .yaml.lock file to add the latest/specific changeset revision for the tool. You can use python scripts/update-tool.py --owner <repo-owner> --name <repo-name> <file.yaml.lock> in order to do this if you just want to add the latest revision.
  • Open a pull request

Requesting a New Tool

  • If you just want the latest version:
    • Edit the .yaml file to add name/owner/section
  • If you want a specific version:
    • Edit the .yaml file to add name/owner/section
    • Run make fix
    • Edit the .yaml.lock to correct the version number.
  • Open a pull request

For UseGalaxy.* Instance Administrators

Set the environment variables GALAXY_SERVER_URL and GALAXY_API_KEY and run make install. This will install ALL of the tools from the .lock files. Be sure that the tool panel sections are pre-existing or it will make a mess of your tool panel. You can run grep -o -h 'tool_panel_section_label:.*' *.yaml.lock | sort -u for a list of categories.

On UseGalaxy.eu

Currently, UseGalaxy.eu runs this on our Jenkins server. Every saturday morning it wakes up early and updates all IUC owned tools + ensures that all the yaml files are installed to usegalaxy.eu.