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
Complete Apollo installation and configuration instructions are available from the Apollo documentation pages
The User's Guide provides guidance on how to use it. Please feel free to update this documentation.
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.
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:
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
or in two terminals:
apollo run-local gradlew devmode
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