- Add a new R script
- Tag data and configure parameters
- Setup a new runnable analysis
- Galaxy and Cloud
- Cheat sheet for R scripting
- Installation instructions
- Manage users and permissions
- Manage database and storage
- Server/development installation
- Setup job submission
xQTL workbench - Installation instructions
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 Windows download and start
- Download xqtl_workbench.zip
- Extract the content of the ZIP inside a folder named xqtl_workbench or so
- Doubleclick run.bat (unblock when asked) to start the application
Typical Linux download and start
chmod u+x run.sh
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. Go to http://localhost:8080/xqtl/ 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.
|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|
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:
Operating system support
|Windows (XP, Vista, 7)||Yes|
|Mac OS X (10.5/6/7)||Yes|