UEA sRNA Workbench

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The UEA sRNA workbench is a simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample small RNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data.




Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of sRNAworkbench and load default version of sRNAworkbench as

module avail sRNAworkbench/ # list available modules
module load sRNAworkbench   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail sRNAworkbench

and choose explicit version you want to use. Load the relevant module and run the UEA sRNA workbench application. The application requires a graphical interface.

$ module add sRNAworkbench3.0
$ start_sRNAworkbench3.0

Tools that the UEA sRNA workbench consists of can be used also separately from command line, though. In order to do that, you'll probably need to load module to run Java (which is otherwise added by start_sRNAworkbench3.0 starting script.

$ module add jdk-7 # load Java module
$ java -jar /software/sRNAworkbench3.0/srna-workbenchV3.0_L/Workbench.jar -tool <toolname>

Example of starting 'mircat' tool:

$ module add jdk-7 # load Java module 
$ java -jar /software/sRNAworkbench3.0/srna-workbenchV3.0_L/Workbench.jar -tool mircat -srna_file <srna-file> -genome <genome-file> [-params <params-file>]

Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.


The UEA sRNA workbench documentation is available on the official producer's webpage


URL: http://srna-workbench.cmp.uea.ac.uk