Installation

Installing and configuring CellBase consists of different steps, as you will see in this page you must first make sure that the server(s) have all dependencies installed, then you can configure and complete the CellBase build.

Overview

Building a CellBase instance has three stages:

This document will show you how to create a CellBase instance. First, you will download a set of raw files from several data sources. These raw files shall contain the core data that will populate the Cellbase knowledgebase. Then, you will build the JSON documents that should be loaded into the Cellbase knowledgebase. These three stages are described in detail below.

** We have already downloaded and processed these data, and the resulting JSON documents are available through our FTP server. For those users who wish to skip these two sections, directly download json documents from http://bioinfo.hpc.cam.ac.uk/downloads/cellbase/v4/homo_sapiens_grch37/mongodb/ and jump to the [[Load Data Models]] section.

Step 1 - Configuring the Server

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 XXX GB of RAM.

Software Dependencies

Below are the software dependencies required by CellBase.

• 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.

Step 2 - Getting CellBase

There are two 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.

Here you can learn more about these two 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

and download the file cellbase-4.7.1.tar.gz from the Downloads section.

Step 3 - Downloading the data

Run this command to download all the data:

$ ./build/bin/cellbase-admin.sh download -d gene -s hsapiens

See Download Sources for the details on all the data that's available to download.

Step 4 - Building the data

Run this command to download all the data:

$ ./build/bin/cellbase-admin.sh build -d gene -s hsapiens

See Building the CellBase database for the details on how to build.

Step 5 - Loading the data

Run this command to download all the data:

$ ./build/bin/cellbase-admin.sh load -d gene -s hsapiens

See Load Data for the details on all the data that's available to download.

Step 6 - Web services

Make sure Tomcat is running, then copy the WAR file the build has created for you into Tomcat's webapps directory:

cp ./build/cellbase-5.0.0-SNAPSHOT.war ~/apache-tomcat-8.5.47/webapps/

You should see the generated API docs here:

http://localhost:8080/cellbase-5.0.0-SNAPSHOT/webservices/

For how to configure tomcat see <HERE>. Includes which database is being used.

See Using CellBase  for information how to run queries.