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Download and Installation
This tutorial is intended to explain how to download and install CellBase and RESTful web services. To learn how to clone and build CellBase please visit README
You can get stable CellBase software in two different ways:
- You can download a built version packaged in a tar.gz from GitHub releases. This is the recommended way for using stable releases.
- or, you can download source code by cloning the repository and following the README documentation to build CellBase, this is useful for testing or trying the last features from the development branch of CellBase, notice you should not use this for production.
To download most featured Cellbase version click here CellBase v3.2.0
To clone and build CellBase from sources you will need Git and Maven. After executing Maven, CellBase will be built in cellbase-app/build folder and it should contain the same files and folders that the built versions at GitHub releases
CellBase has been developed and tested under GNU/Linux Mac operating system. It is mainly written in Java so it should work under Windows.
To run CellBase CLI and web services you will need Java 8+. To execute download command from CLI you will also need Perl and Ensembl API installed since it is used to get some information. Currently CellBase needs MongoDB 2.6+ as a database. We recommend using Tomcat 7+ for installing Java Web Services.
It is good practice to install the content of the tar.gz or cellbase/build folder in a directory. This directory can be located wherever you want, typically in your home or in /opt folders. In this tutorial we are going to install CellBase in your home folder, you can create a folder called cellbase and then uncompress and copy the contents by executing:
mkdir cellbase
tar -zxvf cellbase-XXX.tar.gz
cp -r cellbase-XXX ~/cellbase
You can test the installation by executing from ~/cellbase:
./bin/cellbase.sh -h
A help should be printed.
A .war file can be found within the cellbase/build directory. Move cellbase.war to the appropriate Tomcat directory, for example:
cp /tmp/cellbase/build/cellbase.war /var/lib/tomcat7/webapps/
Check correct deployment:
prompt$ tail /var/log/tomcat7/catalina.out
INFO: Deploying web application archive /var/lib/tomcat7/webapps/cellbase.war
Feb 20, 2015 2:02:34 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat7/webapps/cellbase.war has finished in 4,192 ms