Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/gmod/apollo
Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
https://github.com/gmod/apollo
apollo genome-annotation-editor grails groovy gwt jbrowse jbrowse-plugin
Last synced: 6 days ago
JSON representation
Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
- Host: GitHub
- URL: https://github.com/gmod/apollo
- Owner: GMOD
- License: other
- Created: 2013-10-10T13:05:28.000Z (about 11 years ago)
- Default Branch: develop
- Last Pushed: 2023-12-07T20:08:13.000Z (about 1 year ago)
- Last Synced: 2024-12-19T00:08:17.840Z (6 days ago)
- Topics: apollo, genome-annotation-editor, grails, groovy, gwt, jbrowse, jbrowse-plugin
- Language: Groovy
- Homepage: http://genomearchitect.readthedocs.io/
- Size: 176 MB
- Stars: 129
- Watchers: 37
- Forks: 85
- Open Issues: 237
-
Metadata Files:
- Readme: README.md
- Changelog: ChangeLog.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: docs/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# Apollo
[](https://doi.org/10.5281/zenodo.3555454)
[](https://genomearchitect.readthedocs.org/en/latest/)
[](https://gitter.im/GMOD/Apollo?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
[](https://opensource.org/licenses/BSD-2-Clause)
[](docs/CODE_OF_CONDUCT.md)
### [ Download the latest release](https://github.com/GMOD/Apollo/releases/latest) 
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.`
Questions / Comments / Community contact can be sent to our [Apollo user mailing list](mailto:[email protected]) or posted directory to our [google group](https://groups.google.com/a/lbl.gov/forum/#!forum/apollo). Old questions are [archived on Nabble](http://gmod.827538.n3.nabble.com/Apollo-f815553.html).
Complete Apollo installation and configuration instructions are available from the [Apollo documentation pages](http://genomearchitect.readthedocs.io/en/latest/)
The Apollo client is implemented as a plugin for [JBrowse](http://jbrowse.org). Additional JBrowse plugins may be found in the [JBrowse registry](https://gmod.github.io/jbrowse-registry/) and configured in ```apollo-config.groovy```.
We provide a [Demonstration Apollo](docs/Demo.md) site and an integrated service is provided by [UseGalaxy Europe](https://usegalaxy.eu/).
The [User's Guide](docs/UsersGuide.md) provides guidance on how to use it. Please feel free to update this documentation.
## Setup guide
We provide a [Setup guide](docs/Setup.md) for deploying a [configuring](docs/Configure.md) a production instance.
Launchable public Amazon Web Services (AWS) EC2 images may be [launched from Community AMIs in the N. Virginia region under 'Apollo'](docs/images/EC2Image.png).
Specific information for [setting up AWS instances](docs/Aws_setup.md) is provided for 2.4.1 instances.
Apollo may be launched from [Docker](docs/Docker.md) as well.
The [guide for developers](docs/Apollo2Build.md) shows how to get started with Apollo.
## Web Services
[Python library over web services](https://pypi.org/project/apollo/) and other [web services examples](https://github.com/GMOD/Apollo/tree/develop/docs/web_services/examples).
## Migrating data from older versions
You can follow steps in our [migration guide](docs/Migration.md) 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](docs/Apollo2Build.md) 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
[](https://www.yourkit.com/)
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.