Using the Workbench

Running the sRNA Workbench in GUI mode

In order to run the sRNA Workbench in GUI mode, simply extract all the files from your downloaded zip archive to a new directory, then launch the sRNAWorkbenchStartup.jar. If running on Windows and you launch this jar but get no response there may be a slight problem with your java configuration. In this instance please launch the startup program from the command line using the command:

java -jar sRNAWorkbenchStartup.jar

This will scan your system for available memory and allocate a portion of it to the Workbench.

In the even that the startup program hangs or does not give enough memory for the job you can configure this by hand using the following command:

java -Xms$g -Xmx$g -jar Workbench.jar

Replace the $ symbol with the amount of RAM in GB you wish to assign to the workbench

For detailed instructions on each tool, please visit the Individual Tools or  Workflows pages. Or for a quick overview on what the UEA sRNA Workbench can do and which tool you should select for the task then please visit this page. If you need help navigating to the directory and launching the program in this way please leave a comment and we will reply as soon as possible.

Alternatively, detailed help on each tool can be found from the “Help” menu when running the sRNA Workbench.

Running the sRNA Workbench from the command line

In order to execute the sRNA Workbench from the command line, navigate to the directory that you extracted the sRNA Workbench files to. Then type:

java -jar Workbench.jar -tool <toolname>

where <toolname> is the name of the tool you wish to use.

For each tool if no options are entered, the usage instructions will be printed to the command line. Note: parameters in square brackets are optional.

An example of a complete instruction is given below:

java -jar Workbench.jar -tool mircat -srna_file <srna-file> -genome <genome-file> [-params <params-file>]

 

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices