Apollo

On GitHub

An instantaneous, collaborative, genome annotation editor. The stack is a Java web application / database backend and a Javascript client that runs in a web browser as a JBrowse plugin.

For general information on Web Apollo, go to: http://genomearchitect.org/

Complete Web Apollo installation and configuration instructions are available at: http://webapollo.readthedocs.org

The Web Apollo client is implemented as a plugin for JBrowse, for more information on JBrowse, please visit: http://jbrowse.org

Please note repository update

As of 15-April-2015 the mainline is our 2.0 code. The 1.0 code has now moved to a 1.0 branch.

Quick Update Guide to Version 2.0.x

If you already have Web Apollo instances running, you can use your current JBrowse data directories.

See the Apollo2 build guide to get the proper build guides up.

Migrating data from <2.0:

We are working towards providing data migration scripts that pull data from Apollo 1 to Apollo 2.

Remove any symlinks in your deploy directory if updating from <1.0 version

In your deployment / webapp directory, remove your symlinks. Tomcat will remove data through the symlinks. You won't need symlinks or to deploy the war file.

Important Note: the JBrowse data directory should not be stored in the Tomcat webapps directory. This can result in data loss when doing undeploy operations in Tomcat.

Generate a war file

Most users will only need to generate a war file (for example target/apollo-1.0.2.war) that will be copied into their tomcat webapps directory:

apollo deploy 

Run locally

To run tomcat on 8080:

apollo run-local

Run locally for GWT development

apollo devmode 

Thanks to

![YourKit] (https://www.yourkit.com/images/yklogo.png)

Thanks to YourKit for providing us the use of their YourKit Java Profiler. YourKit supports Open Source.