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-- Apollo latest Installing Apollo Setup guide Using Docker to Run Apollo Apollo Configuration 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 Demo User’s Guide Permissions guide Developing Apollo Developer’s guide How to contribute code to Apollo Automated testing architecture Architecture notes Command line tools Web Service API Apollo Docs » Apollo Edit on GitHub 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 Pre-requisites Deploy the application Detailed build instructions Using Docker to Run Apollo Running the Container Quickstart Production Apollo Run-time OPTIONS Apollo Configuration Main configuration 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 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 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 Phone Home Only owners can edit 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 Automated Configuration and upload Manual Configuration 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 Example Build Script on Unix with MySQL Setup apollo mysql user and database Configure apollo for mysql. If a pre-installed instance: Prepare JBrowse data Adding OpenID Connect Authentication to Apollo Overview Architecture Configuration Maintaining administrator access 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: Using Apollo Demo User’s Guide General Information Navigation Annotation The Information Editor (No need for) Saving your Annotations Exporting Data Public Demo Additional Information About Apollo Permissions guide Global Organism Developing Apollo Developer’s guide Java / JDK Node.js / NPM Grails / Groovy / Gradle (optional) Get the code Verify install requirements Running the code Create server documentation Setting up the application Conclusion 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 Automated testing architecture Notes about the test suites: Chado Architecture notes Overview and developer’s guide Overview Basic layout Schema/domain classes Running the application Main configuration GWT web-app Tests Command line tools Overview Web Service API Warning Examples Python Client What is the Web Service API? Web Services API Next © Copyright 2019, Apollo Revision 95feacf6 . Built with Sphinx using a theme provided by Read the Docs . Read the Docs v: latest Versions latest stable 2.0.8 2.0.6 2.0.5 2.0.4 2.0.3 2.0.2 2.0.1 2.0.0 1.0.4 Downloads html On Read the Docs Project Home Builds Free document hosting provided by Read the Docs ....