This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Galaxy Issue Management

The purpose of this document is to formalize how we manage the full cycle (reporting, tracking progress, resolution) of both feature/enhancement ideas and bugs, as well as providing a few general guidelines for longer term planning for various Galaxy related projects. Some inspiration taken from the way the Docker project labels issues.

Issue Reporting

Issues (bugs, feature requests, etc.) should be reported at GitHub issues, and handling of issues follows the procedures described in the issues document.


Every pull request should, prior to merge, be assigned to the milestone corresponding to the Galaxy release it will first appear in (15.10, 16.01, and so on). This, along with the tags applied, will be used to generate the release notes.

Any non-PR issue assigned to a milestone must be resolved or reassigned prior to publishing that release. This is the primary mechanism by which we force reconciliation (issue/bug fixed, closed, or intentionally postponed) prior to release, and prevent things falling through the cracks. In practice, bugs should almost always be tagged with a milestone which forces the reconciliation date. Issues may be, but they don’t necessarily have to be – this is subjective and it depends on whether or not the issue should be revisited prior to the corresponding release.

Effective use of milestones should prevent bugs from falling through the cracks, and will provide a mechanism for forcing the revisitation(and thus progress or even potential discard) of ideas for enhancements or features.

Deferring Issues

To prevent the review of issues attached to milestones from becoming too cumbersome, and to encourage active review and handling of issues, any contributor can choose to ‘defer’ an issue attached to an upcoming release milestone to a later one. To do this, simply reassign the issue to the new milestone and leave a comment so that others notice, something like ‘Issue deferred to target_milestone_reference, does not block release current_milestone_reference’.

Once deferred, an issue can’t simply be reattached back to the earlier milestone – this requires a PR. The intent here is to make it such that if a contributor wants to force an issue to be handle with a release, they need to put the work forward to do so or convince someone else to.

Labeling Structure

To allow for easy search, filtering, and general issue management every issue or PR (not tagged procedures or planning) is expected to have two labels which indicate the type (kind/) and focus area (area/) of the issue. Any issue without these tags will automatically have a triage label applied indicating that it needs human intervention to be correctly tagged. These triage tagged issues will be regularly reviewed and tagged as appropriate.

Kind Labels

The kind label set is used for classifying the type of contribution or request/report to separate enhancements and new features from bugs, etc.

  • kind/bug - something is broken, and it needs fixing
  • kind/enhancement - polish to an existing feature or interface
  • kind/feature - something brand new
  • kind/refactoring - cleanup or refactoring of existing code, no functional changes

Status Labels

The default status of an issue or PR is ready for review. If that is not true the state should be communicated using the following labels:

  • status/planning - the issue planning phase, this issue may potentially need more information (or just more thinking) to proceed to a work in progress
  • status/WIP - this issue or PR is currently being worked on and in the case of a PR, it should not be merged until this tag is removed

Note that there are no status/complete, status/wontfix, status/duplicate, or other terminal status indicators. This is intentional to keep the tail end of bookkeeping from getting onerous. These sorts of terminal states and their justifications (e.g. the reason why it’s a wontfix, or a reference to the duplicate issue) should be indicated in the closing comment by the issue closer.

Area Labels

The area label is used for tagging issues and pull requests to a particular focus area. This allows for easy searching within that particular domain, as well as more organized release notes.

  • area/admin - Changes to admin functionality of the Galaxy webapp
  • area/API
  • area/auth - Authentication and authorization
  • area/client-build
  • area/compliance
  • area/configuration - Galaxy’s configuration system
  • area/cwl - changes related to supporting the common workflow language in Galaxy
  • area/database - Change requires a modification to Galaxy’s database
  • area/dataset-collections
  • area/datatypes - Changes to Galaxy’s datatypes
  • area/datatype-framework - Changes to Galaxy’s datatype and metadata framework
  • area/dependencies - Changes related to Python or JavaScript dependencies of Galaxy itself
  • area/documentation
  • area/framework
  • area/GIEs
  • area/histories
  • area/i18n - Internationalization and localization
  • area/jobs
  • area/libraries - Change related to data libraries
  • area/objectstore
  • area/performance
  • area/reports
  • area/security
  • area/scripts - Changes to scripts used to run or manage Galaxy.
  • area/testing
  • area/testing/api
  • area/testing/integration
  • area/testing/selenium
  • area/tool-framework
  • area/tool-dependencies - Changes to dependency resolution (including Conda)
  • area/tools - Changes to specific tools in Galaxy
  • area/toolshed- Changes to the Tool Shed client or server
  • area/UI-UX
  • area/upload
  • area/util
  • area/visualizations
  • area/webhooks
  • area/workflows
  • area/workflows/subworkflows

New labels should be proposed by opening a pull request against this document in the dev branch of Galaxy.

Other Useful Labels

While the three labels sets indicating kind, status, and area are required there are several other labels that are be useful and/or have special purpose.

  • procedures is a special tag that indicates that the issue is related to project governance, and it overrides the need for the trio of kind/status/area tags, and these are never auto-flagged for triage. More details are available in the ORGANIZATION document.
  • planning is also a special tag that indicates the issue is related to larger-scale issue planning. These issues are typically meta-issues containing checklists and references to other issues which are subcomponents and stepping stones necessary for issue resolution. These can utilize the area/* tags but are not required to. Status and type make little sense here.
  • friendliness/beginner can be used to indicate a nice entry-level issue that only requires limited understanding of the larger Galaxy framework and ecosystem. This is useful for encouraging new contributors.
  • friendliness/intermediate can be used to indicate an advanced level issue that requires decent understanding of the larger Galaxy framework and system.
  • friendliness/unfriendly can be used to mark issues that require deep understanding of the framework and/or exquisite programming abilities.
  • minor is a special tag used to generate release notes. It should only be applied to pull requests made by committers that fix functionality modified during the same release cycle. Such fixes are unimportant for release notes. No pull request issued by someone outside the committers group should have this tag applied because these pull requests must be highlighted in the release notes.
  • major is a special tag used to generate release notes. In practice this should be applied to at most a couple dozen pull requests each release and is used to prioritize important items of note for the top of release notes sections.
  • merge tag used to indicate PR that only merges a change that has been previously added. Used to filter things out of release notes.
  • feature-request is used to indicate a request for change or feature.
  • triage is a tag automatically added by a GalaxyBot to indicate that the issue needs to be evaluated and properly tagged.
  • hacktoberfest is a tag that encourages contributions to Galaxy codebase by including these issues in the Hacktoberfest event. Similar to friendliness/beginner tag in other characteristics.

The Roadmap

We will maintain a single roadmap GitHub project which will describe (at a very high level) the current major areas of focus for the project. This project will link to issues and PRs, which will go into much more detail and might link to other sub-issues, projects, or PRs.

This roadmap project is subject to periodic review every release.

The current roadmap project is here.


Users can vote for issues by commenting with a +1. It’s possible to sort the issue list by ‘most commented’ which would be a good indicator of what issues are ‘hot’, though this doesn’t necessarily indicate a high vote. It’s possible that that this is good enough and in some ways potentially more useful to find ‘hot’ issues than a flat vote count.


For now, we will rely on a few simple automation rules:

  • All PRs, unless tagged procedures or planning will automatically be tagged triage, indicating that they require attention.
  • All PRs that are not assigned to a milestone will be tagged triage to indicate that they require attention prior to merge.