Apollo¶
Apollo - A collaborative, real-time, genome annotation web-based editor.
The application’s technology stack includes a Grails-based Java web application with flexible database backends and a Javascript client that runs in a web browser as a JBrowse plugin.
You can find the latest release here: https://github.com/GMOD/Apollo/releases/latest and our setup guide: http://genomearchitect.readthedocs.io/en/latest/Setup.html
- Apollo general documentation: http://genomearchitect.github.io/
- JBrowse general documentation: http://jbrowse.org
- Citing Apollo: Dunn, N. A. et al. Apollo: Democratizing genome annotation. PLoS Comput. Biol. 15, e1006790 (2019)
Note: This documentation covers release versions 2.x of Apollo. For the 1.0.4 installation please refer to the installation guide found at http://genomearchitect.readthedocs.io/en/1.0.4/
Contents:
Installing Apollo
- Setup guide
- Using Docker to Run Apollo
- Apollo Configuration
- Main configuration
- Suppress calculation of non-canonical splice sites
- Count annotations
- Suppress add merged comments
- JBrowse Plugins and Configuration
- Translation tables
- Configuring Transcript Overlapper
- Logging configuration
- Add attribute for the original id of the object
- Canned Elements
- Search tools
- Data adapters
- Supported annotation types
- Modify CORS
- Set the default biotype for dragging up evidence
- Apache / Nginx configuration
- Installing secure certificates.
- If Tomcat is running SSL
- Adding extra tabs
- Upgrading existing instances
- Register admin in configuration
- Other authentication strategies
- URL modifications
- Linking to annotations
- Setting default track list behavior
- Set Common Data Directory in the config
- Adding tracks via addStores
- Setting Track Style by type
- Hiding JBrowse tracks from the public
- Only owners can edit
- Chado Export Configuration
- Data generation pipeline
- Troubleshooting guide
- Example Build Script on Unix with MySQL
- Adding OpenID Connect Authentication to Apollo
- Migration guide
Using Apollo