For general and technical information on the Codex, please, refer to the main Readme file
Any Galaxy Community can be added to this project and benefit from the dedicated resources.
Learn how to add your community in the dedicated GTN learning pathway.
To generate interactive tables that can be embedded into subdomains and websites, follow the different tutorials:
To generate a Galaxy Lab for your community, you can
- Follow the dedication tutorial,
- Read the Galaxy Labs Engine documentation.
There is a folder all with all the tools, workflows, and tutorials extracted weekly from public databases.
Then, each community have their own folder, with a specific organization, with community-specific resources necessary for generating the codex (catalogs and labs). To learn how to create a codex for your community, follow the steps explained in the Learning Pathway available above.
The list of tools included in the tool table contains tools from selected ToolShed categories, automatically pulled from the Galaxy ToolShed on a weekly basis.
| Column | Description |
|---|---|
| Suite ID | ID of Galaxy suite |
| Tool IDs | List of Galaxy tool IDs |
| Description | Description of the suite |
| Suite first commit date | |
| 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 |
| Suite parsed folder | |
| 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 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 |
| Related Workflows | Workflows that use at least one tool of the suite |
| Related Tutorials | Tutorials that use at least one tool of the suite |
| To keep | Status to add to a tool after review by a domain expert (True / False) |
| Deprecated | Status to add to a tool after review by a domain expert (True / False) |
The list of tutorials included in the tutorial table contains tutorials with selected tags, automatically pulled from the Galaxy Training Network on a weekly basis.
| Column | Description |
|---|---|
| Topic | Topic associated to the tutorial |
| Title | Title of the tutorial |
| Link | Link to the Tutorial on the GTN |
| EDAM topic | EDAM topics extracted |
| EDAM operation | EDAM operations extracted |
| Creation | Date of creation |
| Last modification | Date of last modification |
| Version | Version of the tutorial |
| Tutorial | Does this tutorial includes a tutorial? (True / False) |
| Slides | Does this tutorial includes slides? (True / False) |
| Video | Does this tutorial includes a video? (True / False) |
| Workflows | Does this tutorial includes a workflow? (True / False) |
| Tools | List of tools included in the tutorial |
| Servers with precise tool versions | List of Galaxy servers with tools available with the version specified in the tutorial |
| Servers with tool but different versions | List of Galaxy servers with tools available in a different version from the one specified in the tutorial |
| Feedback number | Number of feedback |
| Feedback mean note | Mean note of the tutorial |
| Visitors | Number of visitors |
| Page views | Number of page views |
| Visit duration | Mean visit duration |
| Video views | Number of times the video was viewed |
The list of workflows included in the workflow table contains workflows with specific tags, automatically pulled from the public Galaxy instances and WorkflowHub on a weekly basis.
| Column | Description |
|---|---|
| Name | Workflow name |
| Source | Workflow source (i.e. WorkflowHub, galaxy instance name, etc) |
| ID | Workflow unique ID |
| Link | Link to the workflow |
| Creators | Creator full names (when available) |
| Tags | Tags associated to the workflow |
| Creation time | Date of workflow creation |
| Update time | Date of the last update to the workflow |
| Latest version | Latest version |
| Versions | Number of versions |
| Number of steps | |
| Tools | List of tools used by the workflow |
| EDAM operations | |
| EDAM topics | |
| License | |
| DOI | |
| Projects | |
| To keep | Status to add to a workflow after review by a domain expert (True / False) |
| Deprecated | Status to add to a workflow after review by a domain expert (True / False) |