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Installation

This document describes the installation of the viveur software package on an Ubuntu 13.04 installation.

Required Software

  • python2.7 (this is default) and the dev headers apt-get install python-dev

  • libxml2 dev headers apt-get install libxml2-dev libxslt1-dev

  • Apache Ant (1.8 or higher) apt-get install ant

  • MySQL 5.1 (or higher) apt-get install mysql-client mysql-server

  • Oracle Java 6 SDK (it needs to be this specific version)

You will need to download this from Oracle, then use update-alternatives to register (google for a howto)

  • Oracle InstantClient You will need to download this from Oracle, and manual install (in /opt/ or somewhere else)

Setuptools

The version of setuptools that comes with Ubuntu is probably lower then version 0.7. You can try to work around this by using virtualenv --no-setuptools, but there can still be issues finding dependencies. I suggest updating the systemwide setuptools version using the command:

sudo pip install -U distribute

If pip is not installed on the system you can do an apt-get install python-pip

Configuring MySQL

Create a database for the vivo content. The username, password and database name should be entered in the [config] section of the buildout.cfg file.

CREATE DATABASE vivo CHARACTER SET utf8;
GRANT ALL ON vivo.* TO 'vivo'@'localhost' IDENTIFIED BY 'password';

Configure Oracle Instantclient

Not much to do here, but you must export the paths to Oracle instantclient otherwise the software will fail to connect. You might want to put the lines below in your .bashrc profile

export ORACLE_HOME=/opt/oracle/instantclient_11_2
export LD_LIBRARY_PATH=/opt/oracle/instantclient_11_2

Installing the Viveur Software

The software itself can be downloaded from github. It uses buildout to download download and configure tomcat/vivo Issue the following commands:

git clone http://github.com/jascoul/viveur
cd viveur
mv buildout.cfg.in buildout.cfg

Now edit the [config] and [metis] section of the buildout.cfg file Also be sure to export the Oracle path as described in "Configure Oracle Instantclient"

Next we create the python environment where the software will be installed

python bootstrap.py

In the last and final step all dependencies will be downloaded/installed. This will take some time as it will compile cython/lxml and configure vivo with ant

./bin/buildout

For more information on how to use the software see the USAGE file