Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Rename tool columns and add documentation #222

Merged
merged 1 commit into from
Nov 6, 2024
Merged

Rename tool columns and add documentation #222

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
40 changes: 38 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,43 @@ Galaxy Codex

Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools, training, workflows) that can be filtered for any community.

This repository stores the sources to build this catalog. The catalog is automatically updated every week.

This repository stores the sources to build this catalog and its content. The catalog is automatically updated every week.

Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN tutorial**.

# Catalog content

## Tool table

Column | Description
--- | ---
Suite ID | ID of Galaxy suite
Tool IDs | List of Galaxy tool IDs
Description | Description of the suite
Homepage | Homepage for tool
Suite version | Version of the Galaxy suite
Suite Conda package | Conda package used as requirement for the suite
Latest suite conda package version | Latest Conda package version on anaconda
Suite version status | Update status derived by comparing the suite version to the latest conda package version
ToolShed categories |
EDAM operations | EDAM operations extracted using bio.tools
EDAM reduced operations | EDAM operations where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed
EDAM topics | EDAM topics extracted using bio.tools
EDAM reduced topics | EDAM topics where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed
Suite owner | Owner of the Galaxy suite
Suite source | Path to the Galaxy suite
bio.tools ID | ID of the bio.tools entry corresponding to the tool
bio.tools name | Name of the bio.tools entry corresponding to the tool
bio.tools description | Description in bio.tools entry corresponding to the tool
bii ID | ID of BII entry corresponding to the tool
Number of tools available on ... | Number of tools available on given Galaxy server
Suite users (last 5 years) on ... | Number of users of the suite in the last 5 years on given Galaxy server
Suite users on ... | Number of users of the suite on given Galaxy server
Suite runs (last 5 years) on ... | Number of runs of the suite tools in the last 5 years on given Galaxy server
Suite runs on ... | Number of runs of the suite tools on given Galaxy server
Suite users (last 5 years) on main servers | Number of users of the suite in the last 5 years on all UseGalaxy servers
Suite users on main servers | Number of users of the suite on all UseGalaxy servers
Suite runs (last 5 years) on main servers | Number of runs of the suite tools in the last 5 years on all UseGalaxy servers
Suite runs on main servers | Number of runs of the suite tools on all UseGalaxy servers
Deprecated | Deprecation status after review by a domain expert
To keep | Status to add to a community after review by a domain expert
Loading