Apollo

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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.

Requirements

• Java 11
• Neo4j 3.5
• Set username / password same as neo4j/testpass or whatever is in application.yml

Launch for development (server only)

./gradlew bootRun 

Confirm it is up:

http://localhost:8080/

Test API

http://localhost:8080/user/loadUsers

Run tests

Only the unit tests run successfully currently.

./grailsw test-app -unit

OR (runs all checks)

./gradlew check 

Functional tests

From https://github.com/GMOD/apollo-gmod-js/

git clone https://github.com/GMOD/apollo-gmod-js/
yarn
yarn test:nowatch

Note that redo.sh script provided to clear and restart from a homebrew installation. Modify, etc, as needed

Run with Docker

 docker build . 
 docker run -it --publish=8888:8080 --publish=7777:7474 <built image>

For pre-built:

 docker run -it --publish=8888:8080 --publish=7777:7474 gmod/apollo3server:latest

Connect at http://localhost:8888/ . . . eg. http://localhost:8888/user/loadUsers

You'll need to kill the docker instance here, for the moment.

Thanks to

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.

Note

Under development . . more details to come.