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xQTL workbench - Installation instructions

To run xQTL, you must have ​Java installed. Also, we highly recommend to install ​R because this enables you to create graphs, run QTL mapping, and so on.

Feel free to download the ​current release.

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
cd xqtl_workbench
wget http://vm7.target.rug.nl/download/xqtl_workbench.zip
unzip xqtl_workbench.zip
chmod u+x run.sh
sh run.sh

Typical Windows download and start

• Create a folder somewhere named e.g. xqtl_workbench
• Download ​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. Click the URL in the webserver window, or open the URL manually in your favourite browser.
• 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'.
• Make your R is on your path.

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

Browser	Compatible	Layout
Internet Explorer	Yes, v.9 tested	Suboptimal
Firefox	Yes, v.3 tested	Optimal
Chrome	Yes, v.15 tested	Suboptimal
Safari	Slow on v.5	Bad
Opera	Yes, v.11 tested	Suboptimal
Camino	Yes, v.2 tested	Optimal

R compatibility

2.10 or lower - Untested, compatibility not guaranteed.
2.11, 2.12, 2.13 - Fully compatible, tested.
2.14 - Compatible, tested. However you may need to install RCurl manually. The install location is the 'libs' folder inside the home dir of your OS user. Example for MS Windows:
install.packages("RCurl",repos="http://www.stats.ox.ac.uk/pub/RWin/",lib="C:/Users/Administrator/libs")

Operating system support

OS	Compatible
Windows (XP, Vista, 7)	Yes
Linux (Ubuntu)	Yes
Mac OS X (10.5/6/7)	Yes