Server Configuration

Before you can start building CellBase, you must first install all required software dependencies.

Hardware

Which sort of hardware you need depends on how much data you need, query load, etc. A full CellBase instance is 1 TB of data, but loading only genomic data is XXX GB. Also loading and querying data is very resource intensive, we recommend at least 8 GB of RAM.

Software Dependencies

Below are the software dependencies required by CellBase.

Software	Version	Purpose
Java	8	Build and use CellBase
MongoDB	3.6	Database
Tomcat	8.5x	REST API
Docker	18	Building Ensembl

• Java - we recommend you use the OpenJDK.

• MongoDB - put your mongo credentials in settings.xml ???

• Tomcat - put your tomcat credentials in settings.xml ???

• Docker - CellBase uses docker to manager the Perl modules required to query Ensembl's Perl API.

Getting the CellBase code

There are three main ways to get CellBase for installation:

You can download the source code from GitHub and use Apache Maven to compile and build it. Or you can download a prebuilt binary from the CellBase GitHub Releases web page, notice that only stable and pre-releases are tagged and prebuilt. Or you can use our Docker image containing the CellBase binaries. Here you can learn more about these options.

Building from Sources

Although most users will use stable prebuilt binaries (see below) there is still the need for different users to compile and build CellBase, for instance to test a development version. You can learn how to build from the source code at Installation Guide > Building from Source Code.

Download Binaries

You can download stable and pre-release (beta and release candidate) versions from CellBase GitHub Releases. You will find a tar.gz file with the name of cellbase and the version, for instance to download CellBase 4.7.1 you can go to the GitHub Release at:

https://github.com/opencb/cellbase/releases/tag/v4.7.1

Download the file cellbase-4.7.1.tar.gz from the Downloads section.

Docker

We also have docker images containing the CellBase binaries, see CellBase at DockerHub. This docker image expects a running MongoDB instance.