[[TracNav(xQTL)]]

= [wiki:xQTL xQTL workbench] - Installation instructions =

To run xQTL, you must have [http://www.java.com/ Java] installed. Also, we highly recommend to install [http://www.r-project.org/ R] because this enables you to create graphs, run QTL mapping, and so on.

Feel free to download either the [http://vm7.target.rug.nl/download/xqtl_workbench.zip stable version] or the [http://vm7.target.rug.nl/download/xqtl_workbench_unstable.zip unstable version]. The first is more tested, but the latter is often more advanced or refined.

Below we provide some examples on how to install xQTL on various operating systems. Keep in mind that these methods are only 'typical' cases and can be used interchangeably. The ZIP files simply contain a bunch of Java classes, of which the main class is '''boot/RunStandalone'''. The start scripts (run.bat / run.sh) are nothing more than a `java -Xmx512m boot/RunStandalone` call.

=== Typical Linux download and start ===
`mkdir xqtl_workbench`[[BR]]
`cd xqtl_workbench`[[BR]]
`wget http://vm7.target.rug.nl/download/xqtl_workbench.zip`[[BR]]
`unzip xqtl_workbench.zip`[[BR]]
`chmod u+x run.sh`[[BR]]
`sh run.sh`[[BR]]

=== Typical Windows download and start ===
* Create a folder somewhere named e.g. ''xqtl_workbench''
* Download [http://vm7.target.rug.nl/download/xqtl_workbench.zip xqtl_workbench.zip]
* Extract the content of the ZIP in your ''xqtl_workbench'' folder
* Doubleclick ''run.bat'' (unblock when asked) to start the application

=== Typical Mac download and start ===
Both the Linux and Windows way of installing works. The Linux style requires some commandline skills and you may need to install tools such as `wget` first.

=== After install, setting up ===

* Start the application.
* After a few moments, you should see the home page with a message telling you the database was created. This means the table structure inserted and some basic metadata was added, such as an 'admin' and 'anonymous' user.
* Log in with user 'admin', password 'admin' at the login screen. You are returned to the home page.
* At the homepage you will see a message that you can now prefill the database with example users, permissions and some data. Doing this is highly recommended.

To run analysis, you should install some R packages into the 'libs' folder located in the home directory of your OS user.
* Go to 'Admin panel' and then 'Install R packages'. Click 'Install' for the packages.
* If this fails, you should perform R package installation manually to this location. Hint: for Linux and Mac, the location is '~/libs'.

Other admin capabilities include:
* 'Database status': perform loading / removing the example data, or resetting the database.
* 'File storage': configure the location where files are stored.
* 'Users and permissions': management of persons, users, groups, permissions and security tokens.
* 'Admin utilities': update or remove jobs and subjobs manually.
* 'Archiver': create database exports in archives (note: just relational data, so no files) or import existing archives. Useful for database migration.


=== Browser support ===
{{{#!html
<table border="1">
<tr><td bgcolor="silver">Browser</td><td bgcolor="silver">Compatible</td><td bgcolor="silver">Layout</td></tr>
<tr><td>Internet Explorer</td><td bgcolor="green">Yes, v.9 tested</td><td bgcolor="orange">Suboptimal</td></tr>
<tr><td>Firefox</td><td bgcolor="green">Yes, v.3 tested</td><td bgcolor="green">Optimal</td></tr>
<tr><td>Chrome</td><td bgcolor="green">Yes, v.15 tested</td><td bgcolor="orange">Suboptimal</td></tr>
<tr><td>Safari</td><td bgcolor="orange">Slow on v.5</td><td bgcolor="red">Bad</td></tr>
<tr><td>Opera</td><td bgcolor="green">Yes, v.11 tested</td><td bgcolor="orange">Suboptimal</td></tr>
<tr><td>Camino</td><td bgcolor="green">Yes, v.2 tested</td><td bgcolor="green">Optimal</td></tr>
</table>
}}}

=== Operating system support ===
{{{#!html
<table border="1">
<tr><td bgcolor="silver">OS</td><td bgcolor="silver">Compatible</td></tr>
<tr><td>Windows (XP, Vista, 7)</td><td bgcolor="green">Yes</td></tr>
<tr><td>Linux (Ubuntu)</td><td bgcolor="green">Yes</td></tr>
<tr><td>Mac OS X (10.5/6/7)</td><td bgcolor="green">Yes</td></tr>
</table>
}}}