rwieck / apollo

Genome annotation editor, with a Java servlet backend and a Javascript client that runs in a web browser as a JBrowse plugin

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 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

Quick Update Guide to Version 1.0.x

If you already have Web Apollo instances running, you can use these steps to update to Version 1.0.x.

Remove any symlinks in your deploy directory

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.

Edit property files and config files before deploying

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.

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 

Users wanting to compile a custom package can refer to the developers guide

Install jbrowse binaries

As part of the installation process, JBrowse scripts are installed to a local directory (./bin) using install_jbrowse.sh:

install_jbrowse.sh 

Run locally

To run tomcat on 8080:

apollo run

To run tomcat on 8080, but open up the debug port on 8000:

apollo debug

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.