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
As of 15-April-2015 the mainline is our 2.0 code. The 1.0 code has now moved to a 1.0 branch.
Apollo 2 is still a project under development, it has not been formally released, and will lack some of the features and stability necessary for annotation.
Version 1.0.4 is the latest, fully-functional version of Apollo and is available for download at https://github.com/GMOD/Apollo/releases/latest
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.
You should be able to migrate most of your annotation data from Apollo 1 to Apollo 2 using our migration guide built upon our web services.
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.
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
To run tomcat on 8080:
apollo run-local
apollo devmode
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Thanks to YourKit for providing us the use of their YourKit Java Profiler. YourKit supports Open Source.