This page was last updated on Tuesday, 01-Nov-2016 14:18:48 CDT

Installation notes for Biomart version 0.9.0

Home Page

0.9.0 Documentation

Prerequisites

Software: Java 1.6, Ant and Git
OS: major Linux distributions
Server: min. one GB memory, three GB for better performance

• $ sudo apt-get install ant

Installation

1. $ ver="0.9.0"
2. $ cd /usr/local/bin
3. $ git clone https://github.com/biomart/BioMart.git --branch $ver
4. $ cd BioMart
5. Optional? No, will not run under java 6 or 8, I needed this:
   $ export JAVA_HOME=/usr/lib/jvm/jdk1.7.0
6. $ ant
7. Configure biomart.properties as described in the documentation page 10+
   $ nano /usr/local/bin/BioMart/dist/biomart.properties
8. Server must be started from BioMart directory see This message
   $ export JAVA_HOME=/usr/lib/jvm/jdk1.7.0 && cd /usr/local/bin/BioMart && dist/scripts/biomart-server.sh start
9. To run the configurator (requires X-session)
   $ /usr/local/bin/BioMart/dist/scripts/martconfigurator.sh
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