Introduction

This document is a summary of the VIVO installation process. For information about this release, consult the VIVO 1.6 Release Announcement. Links to this and other documentation can be found on the support page at VIVOweb.org.

These instructions assume that you are performing a clean install, including emptying an existing database, emptying the VIVO home directory, and removing a previous installation from the Tomcat webapps directory. VIVO may not work as expected if you install over an an earlier version. If you are upgrading an existing service, please consult the Upgrade Instructions for VIVO release 1.6.

The section entitled A simple installation describes a standard, simple installation for those who want to get VIVO up and running. The second called Installation options section describes several choices; some are intended for a full-scale production installation of VIVO, and some are intended for a person who is developing VIVO on their own machine.

A simple installation

This section describes the process of getting VIVO up and running on your computer, for testing or experimentation, or just to gain familiarity with the process.

If you want to install VIVO on a production server, or if you want to develop VIVO code, you should also read the section on Installation options.

Where is VIVO on your computer?

Before beginning the installation, let's look at the four locations on your computer that will hold VIVO.

The VIVO distribution directory

This is created when you unpack the VIVO distribution file (see Download the VIVO source code, below). This is where you will create your build.properties file (see Specify build properties, below), and where you will make any modifications to the VIVO theme or code. You can create this wherever you choose.

VIVO inside Tomcat

When you run the build script to compile and deploy VIVO (see Compile and deploy, below), the files will be deployed to a directory inside Tomcat. This is the actual executing code for VIVO, but you won’t need to look at it or change it. If you need to change VIVO, make the changes in the distribution directory, and run the build script again. Tell the build script where to find Tomcat by setting tomcat.home in the build.properties file (see Specify build properties, below).

The VIVO home directory

This directory contains the runtime configuration properties for VIVO. VIVO will also use this area to store some of its data. Uploaded image files are stored here, and the Solr search index is stored here also. This is also a place for the files or RDF data that will initialize the VIVO knowledge base. You can create this wherever you choose. Tell VIVO where to find the home directory by setting vitro.home in the build.properties file (see Specify build properties, below). You must create this directory before starting VIVO. You must create the runtime.properties file in this directory (see Specify runtime properties, below), and you must ensure that Tomcat has permission to read and write to this directory when it runs.

The VIVO knowledge base

By default, nearly all of the data that you enter into VIVO will be stored in MySQL. The actual location of this data depends on what system you have, and on how you install MySQL (see Install required software, below). but you won’t need to know the location. You will access the data through VIVO, or occasionally through the MySQL client application.

Preparing for VIVO

Install required software

Before installing VIVO, make sure that the following software is installed on the desired machine:

• Java (SE) 1.7.x http://java.sun.com
  • VIVO has not been tested with OpenJDK
• Apache Tomcat 6.x or 7.x http://tomcat.apache.org
• Apache Ant 1.8 or higher, http://ant.apache.org
• MySQL 5.1 or higher, http://www.mysql.com

Be sure to set up the environment variables for JAVA_HOME and ANT_HOME and add the executables to your path, as required. This requirement depends on the operating system you are using. Consult the installation directions from the software support websites.

The following browsers are supported for this release

• Mac:
  • Chrome 30.0.1599.69 and above
  • FireFox 3.6.28, 10.0.12, 24
  • Opera 12.02
  • Safari 5.0.3
• PC:
  • Chrome 25.1364.2 and above
  • FireFox 10.0.12, 24
  • Internet Explorer 8, 9, 10
  • Opera 12.02

Did it work?

You can test the software installation by typing these commands:

java -version
mysql --version
ant -version

Each of these command should print a response that tells you what version is installed. If any of these commands prints an error message, or reports an unexpected version number, you should review your installation.

Create an empty database and a database account

Decide on a database name, username, and password.You will need these values for this step, and again when you Specify runtime properties.

Log into your MySQL server and create a new database in MySQL that uses UTF-8 encoding. At the MySQL command line you can create the database and user with these commands substituting your values for dbname, username, and password. Most of the time, the hostname will be localhost.

CREATE DATABASE dbname CHARACTER SET utf8;
GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';

Building VIVO

Download the VIVO source code

Download the VIVO application source as either rel-1.6.zip or rel-1.6.gz file and unpack it on your web server:
http://vivoweb.org/download

Specify build properties

At the top level of the VIVO distribution directory, copy the file example.build.properties to a file named simply build.properties. Edit the file to suit your installation, as described in the following table.

These properties are used in compiling VIVO and deploying it to Tomcat. They will be incorporated into VIVO when it is compiled. If you want to change these properties at a later date, you will need to stop Tomcat, repeat the Compile and deploy step, and restart Tomcat.

Compile and deploy

In the previous step, you defined the location of the VIVO home directory, by specifying vitro.home in the build.properties file. If that directory does not exist, create it now.

At the command line, from the top level of the VIVO distribution directory, type:

ant all

to build VIVO and deploy to Tomcat's webapps directory.

The build script may run for as much as five minutes, and creates more than 100 lines of output. The process comprises several steps:

• collecting the source files from the distribution directory,
• compiling the Java source code,
• compiling and running unit tests,
• preparing the Solr search engine,
• deploying VIVO and Solr to Tomcat.

Did it work?

The output of the build may include a variety of warning messages. The Java compiler may warn of code that is outdated. Unit tests may produce warning messages, and some tests may be ignored if they do not produce consistent results.

If the output ends with a success message, the build was successful. Proceed to the next step.

If the output ends with a failure message, the build has failed. Find the cause of the failure, fix the problem, and run the script again.

Running VIVO

Configure Tomcat

Set JVM parameters

VIVO copies small sections of your RDF database into memory in order to serve Web requests quickly (the in-memory copy and the underlying database are kept in synch as edits are performed).

VIVO may require more memory than that allocated to Tomcat by default. With most installations of Tomcat, the setenv.sh or setenv.bat file in Tomcat's bin directory is a convenient place to set the memory parameters. If this file does not exist in Tomcat's bin directory, you can create it.
For example:

export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"

This configures Tomcat to allocate an initial heap of 512 megabytes, a maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower values may be sufficient, especially for small test installations.

If an OutOfMemoryError is encountered during VIVO execution, it can be remedied by increasing the heap parameters and restarting Tomcat.

Set security limits

VIVO is a multithreaded web application that may require more threads than are permitted under your Linux installation's default configuration. Ensure that your installation can support the required number of threads by making the following edits to /etc/security/limits.conf:

apache	hard	nproc	400
tomcat6	hard	nproc	1500

Set URI encoding

In order for VIVO to correctly handle international characters, you must configure Tomcat to conform to the URI standard by accepting percent-encoded UTF-8.

Edit Tomcat's conf/server.xml and add the following attribute to each of the Connector elements: URIEncoding="UTF-8".

<Server ...>
  <Service ...>
    <Connector ... URIEncoding="UTF-8"/>
      ...
    </Connector>
  </Service>
</Server>

Take care when creating Context elements

Each of the webapps in the VIVO distribution (VIVO and Solr) includes a "context fragment" file, containing some of the deployment information for that webapp.

Tomcat allows you to override these context fragments by adding Context elements to server.xml. If you decide to do this, be sure that your new Context element includes the necessary deployment parameters from the overridden context fragment.

See the section entitled Running VIVO behind an Apache server for an example of overriding the VIVO context fragment.

Specify runtime properties

The build process in Step 5 created a file called example.runtime.properties in your VIVO home directory (vitro.home in the build.properties file). Rename this file to runtime.properties, and edit the file to suit your installation, as described in the following table.

These properties are loaded when VIVO starts up. If you want to change these properties at a later date, you will need to restart Tomcat for them to take effect. You will not need to repeat Step 5.

Windows: For those installing on Windows operating system, include the windows drive and use the forward slash "/" and not the back slash "\" in the directory locations, e.g. c:/tomcat.

External authentication: If you want to use an external authentication system like Shibboleth or CUWebAuth, you will need to set an additional property in this file. See the step below entitled Using an External Authentication System with VIVO.

    scheme + servername + port + vivo_webapp_name + "solr"

Start Tomcat

Was the installation successful?

Using VIVO

Log in and add RDF data

Set the Contact Email Address

Review the VIVO terms of use

Installation options

Running VIVO behind an Apache server

Using an external authentication system

Developers' installation: obtaining VIVO source code from Git

Customizing VIVO with a "3-tier" build

Using a database other than MySQL

Using a servlet container other than Tomcat

Adding OpenSocial gadgets to VIVO

VIVO in a language other than English

Other installation options