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 for 1.x, 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
Note: For documentation of older Web Apollo versions, please see http://gmod.org/wiki/WebApollo_Installation
If you already have Web Apollo instances running, you can use these steps to update to Version 1.0.x.
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.
cp ./sample_config.properties ./config.properties # must set database parameters and data directories
cp ./sample_config.xml ./config.xml # see configuration guide for more details
cp ./sample_canned_comments.xml ./canned_comments.xml # see configuration guide for more details
cp ./sample_blat_config.xml ./blat_config.xml # optional
cp ./sample_hibernate.xml ./hibernate.xml # optional
cp ./sample_log4j2.json ./log4j2.json # optional
cp ./sample_log4j2-test.json ./log4j2-test.json # optional
You must edit config.properties to supply the jbrowse data and annotations directory. The datastore.directory property is where Web Apollo annotations are to be stored. The jbrowse.data property is where the jbrowse tracks are stored.
If you specify the database properties in both the config.xml and config.properties, only the one in config.properties will be used.
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
Users wanting to compile a custom package can refer to the developers guide
As part of the installation process, JBrowse scripts are installed to a local directory (./bin) using install_jbrowse.sh:
install_jbrowse.sh
To run tomcat on 8080:
apollo run
To run tomcat on 8080, but open up the debug port on 8000:
apollo debug
![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.