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Apollo\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3555454.svg)](https://doi.org/10.5281/zenodo.3555454)\n![Lint](https://github.com/GMOD/Apollo/workflows/Lint/badge.svg)\n![Java CI with Gradle](https://github.com/GMOD/Apollo/workflows/Java%20CI%20with%20Gradle/badge.svg)\n[![Documentation](https://readthedocs.org/projects/genomearchitect/badge/?version=latest)](https://genomearchitect.readthedocs.org/en/latest/)\n[![Chat at Gitter](https://badges.gitter.im/GMOD/Apollo.svg)](https://gitter.im/GMOD/Apollo?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge)\n[![License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)\n[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg?style=for-the-badge\u0026logo=data:image/svg+xml;base64,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)](docs/CODE_OF_CONDUCT.md)\n\n\n### [![](https://github.com/GMOD/Apollo/blob/master/docs/images/download_small.png)\u0026nbsp;Download the latest release](https://github.com/GMOD/Apollo/releases/latest) ![](docs/images/ApolloLogo_100x36.png)\n\nA collaborative, real-time, genome annotation editor.  The stack is a Java web application / database backend and a\nJavascript client that runs in a web browser as a JBrowse plugin.  \n\nCite 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.` \u003chttps://doi.org/10.1371/journal.pcbi.1006790\u003e\n\n\nQuestions / Comments / Community contact can be sent to our [Apollo user mailing list](mailto:apollo@lbl.gov) 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).\n\nComplete Apollo installation and configuration instructions are available from the [Apollo documentation pages](http://genomearchitect.readthedocs.io/en/latest/)\n\nThe 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```.\n\nWe provide a [Demonstration Apollo](docs/Demo.md) site and an integrated service is provided by [UseGalaxy Europe](https://usegalaxy.eu/).\n\nThe [User's Guide](docs/UsersGuide.md) provides guidance on how to use it.  Please feel free to update this documentation.\n\n## Setup guide\n\nWe provide a [Setup guide](docs/Setup.md) for deploying a [configuring](docs/Configure.md) a production instance.  \n\nLaunchable public Amazon Web Services (AWS) EC2 images may be [launched from Community AMIs in the N. Virginia region under 'Apollo'](docs/images/EC2Image.png).  \nSpecific information for [setting up AWS instances](docs/Aws_setup.md) is provided for 2.4.1 instances.\n \nApollo may be launched from [Docker](docs/Docker.md) as well.  \n\nThe [guide for developers](docs/Apollo2Build.md) shows how to get started with Apollo. \n\n## Web Services\n\n[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).\n\n\n## Migrating data from older versions\n\nYou can follow steps in our [migration guide](docs/Migration.md) to move annotations and data from older versions.\n\n### Note about data directories\n\nApollo 2.X allows you to add multiple data directories to your webapp, and it expects the data directories to be stored\noutside of the tomcat webapps directory. Use the [developer's guide](docs/Apollo2Build.md) to learn how to add new\ndata directories for your organisms.\n\n\n**Important Note: All data from a webapps directory will disappear when doing tomcat \"undeploy\" operations, even if\nit is a symlink.**.\n\n\n### Launch Apollo in a temporary server\n\nTo launch Apollo with temporary settings, use the `apollo run-local` command, which will initialize your server\nautomatically with an H2 (zero-configuration) database.\n \n    apollo run-local 8080\n\nIt will also use your custom settings if an apollo-config.groovy file has been setup.\n\n### Generate a war file\n\nUsers can generate a war file (for example target/apollo-1.0.2.war) that will be copied into their tomcat webapps\ndirectory for production deployments:\n\n  apollo deploy \n\nNote: make sure to create an apollo-config.groovy file following the sample data (e.g.\nsample-postgres-apollo-config.groovy) to make sure you use your preferred database settings.\n\n\n### Run locally for GWT development\n\n    apollo devmode \n\nor in two terminals:\n\n    apollo run-local \n\tgradlew devmode \n   \n\n### Thanks to\n\n[![YourKit](https://www.yourkit.com/images/yklogo.png)](https://www.yourkit.com/) \n\nYourKit supports open source projects with innovative and intelligent tools\nfor monitoring and profiling Java and .NET applications.\nYourKit is the creator of \u003ca href=\"https://www.yourkit.com/java/profiler/\"\u003eYourKit Java Profiler\u003c/a\u003e,\n\u003ca href=\"https://www.yourkit.com/.net/profiler/\"\u003eYourKit .NET Profiler\u003c/a\u003e,\nand \u003ca href=\"https://www.yourkit.com/youmonitor/\"\u003eYourKit YouMonitor\u003c/a\u003e.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgmod%2Fapollo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgmod%2Fapollo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgmod%2Fapollo/lists"}