Apollo - A collaborative, real-time, genome annotation web-based editor.
The application’s technology stack includes a Grails-based Java web application with flexible database backends and a Javascript client that runs in a web browser as a JBrowse plugin.
You can find the latest release here: https://github.com/GMOD/Apollo/releases/latest and our setup guide: http://genomearchitect.readthedocs.io/en/latest/Setup.html
This code has been using docker environment based in a image from Project owner. The project has some customizations to share directorys between host and container. The share was made to facilitate the add of news Organism and make backup actions easier.
Open the Terminal on your Operating System and execute the below command:
Ps: You need be on directory where the project was downloaded. Eg: /Users/Desktop/apollo
docker-compose -f docker-compose.yml -p apollo up -d --buildThe docker create a some directory in root directory. Is important remeber that this code is preparate to running in Windows environment and this root directory is located on "C:". To customize to Unix system please replace the source directory in docker-compose.yml
To do the docker installation on Windows please do the windows update to latest version and after that do the download and installation of Docker from the below link.
# Please click on download the latest WSL2 Linux kernel and do the installation
Linux Kernel : https://docs.microsoft.com/en-us/windows/wsl/wsl2-kernel
# Please do the download and do the installation
Docker: https://hub.docker.com/editions/community/docker-ce-desktop-windows/The default database is Postgresql and in the future we will create a script to do a dump from database.
The URL access is based on 8080 port and is based in Tomcat Webserver. Is possible do a reverse proxy with NGINX or Apache.
The default user is admin@local.host and password is password. It should be replace in the first login.
To create a new organism you should copy the original files to root directory and sub-folder organism like: "C:/apollo/organism/yeast", is important remember that the files should be extracted and must contain the trackList.json file.
In the Apollo sytem in Organism tab to create a new organism the section directory must be /opt/organism/organism_name, i.e: /opt/organism/yeast
To create a new users, you should have a Organism created. The users are authorization options to ensure the correct permissions.