The small RNA Workbench Version 3.1.1

The UEA Small RNA Workbench Version 3.1.1: Released: 04/01/2014

A hot fix release for OSX version 10.8+ (Mountain Lion) and 10.9+ (Mavericks) users only. Full release notes for Version 3.1 can be found here


This release fixes the issues with the original .app file created on OSX 10.7. The issue related to the security update to the OSX program known as Gatekeeper:

This prevented the application stub launcher from working correctly. A completely new stub launcher and plist file is included in this update that should allow the software to work correctly.

IMPORTANT: First time use requires right click on the .app file, then select ‘Open’ to view this screen 

Right Click or CTRL click to show this menu
Right Click or CTRL click to show this men

when asked if you want to run the software, on this screen:Screen Shot 2014-02-04 at 14.33.23press Open.  From then on the software will be trusted and allowed to run as normal

  • SAM

    Hi, I just downloaded the 3.1.1 version and followed these instructions to the letter, to run on a Mid-2010 iMac 27″ with 16GB memory running OSX 10.9.2. It doesnt matter if I try to run through the .dmg mount, or move the workbench to my applications folder, or elsewhere, the app does not load. It will not even appear on my force quit menu after clicking it.

    To solve it, I have to right click the app, select ‘show package contents’, navigate to /Contents/Java and then click on ‘sRNAWorkbenchStartup.jar’. This launched a loader, which also crashed, returning the following error message in XCode:

    “JRELoadError” = “Unable to load Java Runtime Environment.”;
    “MainClassNameRequired” = “Main class name is required.”;
    “JavaDirectoryNotFound” = “Unable to enumerate Java directory contents.”;

    Clicking on ‘Workbench.jar’ then opened a window for initial setup. After inputting my details the workbench did launch, but exiting and attempting to start from the app again failed to launch anything. However, this time clicking on ‘Workbench.jar’ in the /Contents/Java folder did launch the workbench.

    Having done all this, trying

    java -jar sRNAWorkbenchStartup.jar

    in terminal as per quickstart guide got me nowhere either in /, ~ or inside /Applications. If I navigate to /Applications/ and execute the same command the splash appears but it crashes out with the error

    ‘Splash took too long’.
    memory: 11071.281


    ‘java -jar Workbench.jar’

    Returns the following:

    Exception in thread “main” java.lang.UnsupportedClassVersionError: uk/ac/uea/cmp/srnaworkbench/Main : Unsupported major.minor version 51.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClassCond(
    at java.lang.ClassLoader.defineClass(
    at Method)
    at java.lang.ClassLoader.loadClass(
    at sun.misc.Launcher$AppClassLoader.loadClass(
    at java.lang.ClassLoader.loadClass(

    Not sure what is the cause behind this, please post here if you need more attempts at it so that I can help you find the solution. NB, I have a bucketload of bioinformatics apps and dev tools on this rig, all running generally smoothly. There might be some conflict somewhere.

    • The sRNA Workbench

      Hi Sam,

      not sure what has caused this at the moment. We have almost identical systems with the same OS! Could we start by letting me know which java version you have running at the moment? (type java -version into the terminal window) and we can go from there?


      • Fred

        Did this ever get solved, because I’m having the exact same issue.


        • The sRNA Workbench

          Hi Fred,

          I got no further replies on Java version etc so could not progress any further.

          Could you let me know a bit more about your system? Also Java -version text?


          • Fred

            Hi Matt,

            Thanks for the reply. Working on a Mac OsX 10.9.2.

            $ java -version

            java version “1.7.0_55”

            Java(TM) SE Runtime Environment (build 1.7.0_55-b13)

            Java HotSpot(TM) 64-Bit Server VM (build 24.55-b03, mixed mode)

            Meanwhile I’ve trying the perl version but also ran into a few problems (see my other post). Thanks for the help


          • The sRNA Workbench

            Hi Fred,

            It is very difficult to diagnose this one. I have just downloaded the software again, also identical setup. Same java version, same OS version.

            I just double clicked on the icon and it loaded fine after warning me that it is an application downloaded from the internet.

            All I can think to do is go down the the student Apple lab and see if the problem persists over there.

            When you double click on the .app icon is there any messages put out into the ‘Console’ application? If you run that app before running the workbench?


          • aurelie

            Hi is there a solution I have the same problem except when i launch the sRNAWorkbenchStartup.jar for the command line i have this error :

            java[11713] : The function `CGContextErase’ is obsolete and will be removed in an upcoming update. Unfortunately, this application, or a library it uses, is using this obsolete function, and is thereby contributing to an overall degradation of system performance.

            Splash took too long

            memory: 55.847656

            thanks for the answer

          • The sRNA Workbench

            Hi Aurelie,

            Can you confirm which version of java you are using please? Type java -version into the terminal window. Also which OS etc would be useful