Apollo

Apollo - An instantaneous, collaborative, genome annotation 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

For general information on Apollo, go to: https://genomearchitect.github.io/

For more information on JBrowse, please visit: http://jbrowse.org

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:

• Pre-requisites
  • Client pre-requisites
  • Server-side pre-requisites
• Quick-start Developer’s guide
  • Java / JDK
  • Node.js / NPM / Bower
  • Grails / Groovy / Gradle (optional)
  • Get the code
  • Verify install requirements
  • Setting up the application
  • Conclusion
• Setup guide
  • Production pre-requisites
  • Deploy the application
  • Detailed build instructions
• Apollo Configuration
  • Main configuration
  • JBrowse Plugins
  • Translation tables
  • Logging configuration
  • Canned Elements
  • Search tools
  • Data adapters
  • Supported annotation types
  • Apache / Nginx configuration
  • Upgrading existing instances
  • Register admin in configuration
  • Other authentication strategies
  • URL modifications
  • Phone Home
• Chado Export Configuration
  • Create a Chado database
  • Create a Chado user
  • Load Chado schema and ontologies
  • Configure data sources
  • Export via UI
  • Export via web services
• Data generation pipeline
  • prepare-refseqs.pl
  • flatfile-to-json.pl
  • generate-names.pl
  • add-bam-track.pl
  • add-bw-track.pl
  • Customizing different annotation types (advanced)
  • Customizing features
  • Bulk loading annotations to the user annotation track
  • Disable draggable
• Troubleshooting guide
  • Tomcat memory
  • Tomcat permissions
  • Errors with JBrowse
  • Complaints about 8080 being in use
  • Unable to open the h2 / default database for writing
  • Grails cache errors
  • Mysql invalid TimeStamp error
• Migration guide
  • Migration from Evaluation to Production:
  • Migration from 2.0.X to 2.0.Y on production:
  • Migration from 1.0 to 2.0:
• Permissions guide
  • Global
  • Organism
• Automated testing architecture
  • Notes about the test suites:
  • Chado
• How to contribute code to Apollo
  • Audience
  • Basic principles of the Apollo-flavored GitHub Workflow
  • Table of contents
  • One Time Setup - Forking a Shared Repo
  • Typical Development Cycle
  • GitHub Tricks and Tips
  • References and Documentation
• Architecture notes
  • Overview and quick-start
  • Overview
  • Basic layout
  • Schema/domain classes
  • Running the application
  • Main configuration
  • GWT web-app
  • Tests
• Command line tools
  • Overview
• Web Service API
  • What is the Web Service API?
  • Web Services API
• Example Build Script on Unix with MySQL