Skip to content
/ Apollo Public

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

License

Notifications You must be signed in to change notification settings

GMOD/Apollo

Folders and files

NameName
Last commit message
Last commit date

Latest commit

ab12ab4 · Jan 31, 2025
Jan 31, 2025
Jan 31, 2025
May 28, 2021
Apr 27, 2021
Jan 3, 2023
Mar 15, 2016
Jan 3, 2023
May 4, 2016
Mar 21, 2017
Jul 2, 2018
Jul 11, 2022
Apr 28, 2021
Feb 16, 2021
May 12, 2021
Jun 25, 2016
Apr 8, 2016
Aug 25, 2020
Dec 17, 2020
Mar 9, 2018
Jun 25, 2020
Jan 3, 2023
May 3, 2022
Jan 21, 2020
Feb 16, 2021
Jun 22, 2021
Jan 3, 2023
Mar 7, 2019
Jul 10, 2018
Mar 14, 2016
Jun 25, 2016
Dec 17, 2020
Feb 27, 2019
Jan 5, 2021
Jun 18, 2019
May 7, 2021
May 7, 2021
May 7, 2021
Mar 14, 2016
Nov 28, 2017

Repository files navigation

Apollo

DOI Lint Java CI with Gradle Documentation Chat at Gitter License Contributor Covenant

A collaborative, real-time, 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.

Cite Apollo using Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, et al. (2019) Apollo: Democratizing genome annotation. PLoS Comput Biol 15(2): e1006790. https://doi.org/10.1371/journal.pcbi.1006790

Questions / Comments / Community contact can be sent to our Apollo user mailing list or posted directory to our google group. Old questions are archived on Nabble.

Complete Apollo installation and configuration instructions are available from the Apollo documentation pages

The Apollo client is implemented as a plugin for JBrowse. Additional JBrowse plugins may be found in the JBrowse registry and configured in apollo-config.groovy.

We provide a Demonstration Apollo site and an integrated service is provided by UseGalaxy Europe.

The User's Guide provides guidance on how to use it. Please feel free to update this documentation.

Setup guide

We provide a Setup guide for deploying a configuring a production instance.

Launchable public Amazon Web Services (AWS) EC2 images may be launched from Community AMIs in the N. Virginia region under 'Apollo'.
Specific information for setting up AWS instances is provided for 2.4.1 instances.

Apollo may be launched from Docker as well.

The guide for developers shows how to get started with Apollo.

Web Services

Python library over web services and other web services examples.

Migrating data from older versions

You can follow steps in our migration guide to move annotations and data from older versions.

Note about data directories

Apollo 2.X allows you to add multiple data directories to your webapp, and it expects the data directories to be stored outside of the tomcat webapps directory. Use the developer's guide to learn how to add new data directories for your organisms.

Important Note: All data from a webapps directory will disappear when doing tomcat "undeploy" operations, even if it is a symlink..

Launch Apollo in a temporary server

To launch Apollo with temporary settings, use the apollo run-local command, which will initialize your server automatically with an H2 (zero-configuration) database.

apollo run-local 8080

It will also use your custom settings if an apollo-config.groovy file has been setup.

Generate a war file

Users can generate a war file (for example target/apollo-1.0.2.war) that will be copied into their tomcat webapps directory for production deployments:

apollo deploy

Note: make sure to create an apollo-config.groovy file following the sample data (e.g. sample-postgres-apollo-config.groovy) to make sure you use your preferred database settings.

Run locally for GWT development

apollo devmode 

or in two terminals:

apollo run-local 
gradlew devmode 

Thanks to

YourKit

YourKit supports open source projects with innovative and intelligent tools for monitoring and profiling Java and .NET applications. YourKit is the creator of YourKit Java Profiler, YourKit .NET Profiler, and YourKit YouMonitor.