Downloads

The UEA sRNA Workbench has been tested on various platforms including:

  • Mac OSX (Version 10.5 Leopard; 10.6 Snow Leopard; 10.7 Lion, 10.8 Mountain Lion, 10.9 Mavericks, 10.10 Yosemite)
  • Linux (Ubuntu Version 10, 11; CentOS Version 5, 6)
  • Windows 7

Currently the software is built and tested on the official Oracle builds of Java only, in addition, the latest version of JRE (Update 60) has extremely poor javascript performance compared to the older version (Update 51) therefore we strongly recommend using Update 51 for running this software. However, most of the software should behave in the same way under open builds but I cannot guarantee this.

Links to all available downloads can be visited from this page.

An overview of the project download page can be found here.

Download latest version

Version 4.4 Alpha notes

Version 4.3.1 Alpha notes

Version 4.3 Alpha notes

Version 4.2.3 Alpha notes

Version 4.2.2 Alpha notes

Version 4.2 Alpha notes

Version 4.1 Alpha notes

Version 4.0 Alpha notes

Version 3.2 notes

Version 3.1.1 notes

Version 3.1 notes

Version 3.0 notes

Download 3.01 (Alpha) containing an update to our newest tool CoLIde

Download 3.0 (Alpha) containing our newest tool CoLIde

Version 3.0 (Alpha) notes

Version 2.5.0 notes

Version 2.4.2 notes

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Version 2.2 notes

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Version 1.02 notes

Version 1.01 notes

Version 1.0 notes

  • B. Emese

    Hi,
    I’m using sRNA workbench version 3.0, on ubuntu 16.04 with the recommended jre installed.

    When running mirCat, I got no results, not with own, neither with tutorial data (either in GUI or CLI).
    I saved the mirCat log, I assume the problem is with RNAfold (an example part from the mircat log file):

    INFO: MIRCAT: Either RNAfold returned no result or the resulting sequence to be flanked was longer than 25. Ignore
    May 18, 2017 1:22:26 PM uk.ac.uea.cmp.srnaworkbench.utils.LOGGERS.MiRCatLogger log
    WARNING: MIRCAT: RNAfold produced no structure so ignoring

    Thank you in advance for helping!

  • Anjana Raj

    Hi, am trying to use sRNA workbench, latest version. But am unable to run as the console is not running after the sample data and reference genomne are loaded.

    What capacity of RAM is required for running sRNA workbench?

    • The sRNA Workbench

      It depends on the size of the input dataset. The sample data should not use too much RAM.

      • Anjana Raj

        Hi, how to identify adapter sequences in my data, as I am unable to find out the information in my data.

        In few posts, I read the over represented sequences will be the adapter sequences, shall I take it that way and remove those sequences.

  • The sRNA Workbench

    Hi Fuyou,

    Sorry for the delay, for some reason I wasn’t informed automatically that this message was pending!

    Yes this software can run on a server, all that is required is the java runtime (v8+) to be installed on the system then you can run it as normal, either via the command line for the original tools or if you have an X like system installed on both client and server you can use the GUI by forwarding the graphics to your PC.

    Hope this helps,
    Matt

  • Bharti

    Hi
    I want to use sRNA workbench for sRNA analysis. I am facing a problem that when I run java -jar Workbench.jar command I get this error ‘Could not find or load main class uk.ac.uea.cmp.srnaworkbench.MainAppFX’. I am bit new in the field of bioinformatics, so I am not able to understand and correct this error. Can you help with this?
    Thanks

    • The sRNA Workbench

      Hi Bharti,

      Several things could cause this, it is one of those errors that java throws for a variety of reasons.

      Can you let me know what happens when you type java -version into the console?

      Cheers,
      Matt

      • Alex

        Was this error resolved? I am encountering the same error message on my system.

        • The sRNA Workbench

          Hi Alex,

          I didn’t get any more info so couldn’t go further with it.

          Could you copy paste the entire error text you get or email me an image of it?

          Cheers,
          Matt

          • Alex

            This is the error message, Error: Could not find or load main class uk.ac.uea.cmp.srnaworkbench.MainAppFX

            I called it from the command line with this command java -jar ~/srna-workbenchV4.2.1Alpha.D/Workbench.jar -tool mircat -srna_file ~/breakout2.fa -genome ~/editedArabidopsis_thaliana.TAIR10.31.dna.genome.fa
            I have since managed to get mircat running using version 3 of the toolkit.

          • The sRNA Workbench

            Hi Alex,

            Glad to hear you got it to run using a previous version. Just so I can address the problem for others (this is a very early code release and I am trying to fix as much as I can with help from users),

            could you give me some more info? Was that the only thing the software printed out to you? What system are you on? What java version? Are there any spaces in the path that you unpacked the workbench into?

            Thanks for your help!
            Matt

          • Alex

            There are no spaces in the filepath, the java version is 1.8.0_101. I also tried using version 1.7.0.72 which gave this output Exception in thread “main” java.lang.UnsupportedClassVersionError: uk/ac/uea/cmp/srnaworkbench/MainAppFX : Unsupported major.minor version 52.0
            I running this on a linux system.

          • The sRNA Workbench

            Thanks Alex, what flavour of linux was it?

          • Alex

            Red Hat Enterprise Linux Server release 6.6 (Santiago)

          • The sRNA Workbench

            ok thats great. I dont have that installed anywhere but I will stick a version on a test machine and see if I can recreate the error…

          • Alex

            Great, thanks for your help

  • Fuyou Fu

    Hi, I used the UEA small RNA workbench for small RNA analysis. It should be very nice. But my computer RAM is too low to run my data. I have a server with big RAM. Could I use server for running the workbench? How to do it?
    Thanks,
    Fuyou

  • Amanda

    Hi Matt,
    Any chance of getting the workbench for Apple OS x El Capitan 10.11.1?

    My PI loves updating the lab computers.. Alas… workbench won’t start on El Capitan

    • Hi Amanda,

      That is strange, I also am using that exact OS version! It seems ok at my end, which version of the workbench are you using?

      Cheers,
      Matt

  • VIBHA

    the online version of ueasRNA tool kit is not working…I have been trying since days…i need it urgently…pls reply…it is urgent…

    • The sRNA Workbench

      Hi,

      Unfortunately the online version of the tools is no longer officially supported having been replaced with the sRNA Workbench.

      I will try to make it work again at some point but it may take a while (the old cluster that used to run it was decommissioned)

      Is there any thing I can help with in regards to use of the Workbench instead?

      Cheers,
      Matt

  • Chirag Parsania

    Hi,

    I have downloaded .dmg file of sRNA workbench. I copied content folder to my local drive. I have started sRNA workbench using following command. java -jar -Xmx13G -Xms1G workbench.jar

    It started successfully. After that I tried to run mircat. It couldn’t. I check the log file. It shows me following command

    java -Xms32m -Xmx32m -jar …………

    I don’t understand why it’s shows me 32m memory though I have give 13G and 1G.

    Let me know how can I run sRNAworkbench on mac

    Thank you,
    Chirag

    • The sRNA Workbench

      Hi Chirag,

      Dont worry about those messages, the software also boots several small instances of a program designed to run external programs that are required by the workbench and that is what those commands mean (they are starting a program called exemanager).

      Did miRCat give any error messages when you tried to run it?

      Cheers,
      Matt

      • Chirag Parsania

        Hi Matt,

        Thank you for the prompt response.

        Ok I got your point. Now I have one more concern.

        First I tried mircat on 8 GB mac. It gave me java heap space error. So I moved data on server and I run it through command line. Over there I got .patman file but I couldn’t get the sRNA files (known and novel). Now to get sRNA files I run mircat again on mac (16GB RAM) by giving .patman as in input instead of .fastq file. It finished successfully but again I didn’t get any result on my screen.

        I have very nice smal rna length distribution (between 18-44) along with high depth. (Total number of reads are 18 million and number of tags are 5 million). I don’t understand why mircat is not giving any small rna

        Any help would be appreciated

        Thank you
        Chirag.

        • The sRNA Workbench

          Hi Chirag,

          It is difficult to say why you got no results, it could be down to a number of factors, from incorrect parameters to a problem with the software or configuration. Could you email a sample of your input .patman file to me? I am also using a mac. A few hundred lines and a location I can retrieve the genome from and I will see if I can find out why you got nothing back.

          My address is matthew.stocks@uea.ac.uk

          Cheers,
          Matt

          • Chirag Parsania

            Hi Matt,

            Thanks a lot.

            I will send you the data.

            Cheers,
            Chirag

          • Chirag Parsania

            Hi Matt,

            I have tried to send you the data on the address you posted here. but unfortunately I am getting mail sending failure error. Could you please give me alternate address to send you my data ??

            Thanks a lot
            Chirag

          • The sRNA Workbench

            Hi Chirag,

            Not sure why you are getting an error, that is the correct address! What type of error are you getting?

            Alternatively, do you use google drive or dropbox?

            Cheers,
            Matt

          • Chirag Parsania

            Hi Matt,

            I have successfully shared data with you using google drive. Error was because of attachment size.

            Cheers,
            Chirag

          • The sRNA Workbench

            Hi Chirag,

            I have ran the data you sent me and got quite a few results back. I will email you with further details.

            Cheers,
            Matt

          • Chirag Parsania

            Hi Matt,

            As you told I have turned off all the processes which was using Java. After I restarted workbench and ran mircat on the test data. It ran successfully and I got the out file as well. Now I will try with original data set.

            Thank you very much for your time and valuable inputs

            Cheers,
            Chirag

          • The sRNA Workbench

            Hi Chirag,

            No worries, let me know if you have any further issues or questions

            Cheers,
            Matt

      • Chirag Parsania

        Hi Matt,

        Kindly answer my previous query as soon as possible. It’s very urgent for me.

        Thanks a lot in advance

        Chirag

        • The sRNA Workbench

          I have posted up a response, sorry for the delay.

          Cheers,
          Matt

  • The sRNA Workbench

    Hi Tanushree,

    Could you give me a little more info? How much RAM in total does your windows machine have? Also, with the centos system, did you try and run the workbench.jar file directly instead of via the startup? Could you let me know which version of java you have installed on each system? (type java -version into the cmd or terminal respectively)

    Cheers,
    Matt

  • The sRNA Workbench

    Hi,

    The problem may be related to you specifying an output directory as well as a file.

    Try to re-run with just –out a rather than output/a

    let me know if this works for you!

    Cheers,
    Matt

    • Fred

      Hi Matt,

      Thanks for the reply. Isn’t specifying an output directory required as a parameter for –out? Leaving the directory out gave me this:

      $ perl srna-tools.pl –tool adaptor –adaptor_sequence_3 TCGT –out –srna_file files/GSM118373_Rajagopalan_leaf.fa
      #### Please correct parameter input ####
      Parameter –out|outdir (target for result files) is required in command line
      mode (–out)

      cheers
      Fred

      • The sRNA Workbench

        Hi Fred,

        You need to specify the directory name, so the command should read:

        $ perl srna-tools.pl –tool adaptor –adaptor_sequence_3 TCGT –out a –srna_file files/GSM118373_Rajagopalan_leaf.fa

        Cheers,
        Matt

        • Fred

          Hi Matt,

          Copy pasted the command line you posted to no avail:

          $ perl srna-tools.pl –tool adaptor –adaptor_sequence_3 TCGT –out a –srna_file files/GSM118373_Rajagopalan_leaf.fa

          Uncompression of files: pre-processing_input_files

          usage: mv [-f | -i | -n] [-v] source target

          mv [-f | -i | -n] [-v] source … directory

          ########################### sRNA Toolkit ERROR #########################

          An error occurred while running the job: Uncompression of files, error while

          uncompressing files: Problem renaming file

          ; File: /Users/fvanex/UEA BioPerl/srna-tools-cli/lib/SrnaTools/Module/UncompressInfiles.pm;

          Line: 107; Log-msg: –

          To see more details, either activate the ‘debug’ option in the application

          configuration file or check the error logs.

          Best
          Fred

          • The sRNA Workbench

            Hi Fred,

            Just ran a fresh install with the same command using the test data as you have and it seemed to work ok. I can only assume it is an OSX problem (as the tests were carried out on a LINUX machine).

            Unfortunately the scripts and entire package have been developed on a LINUX environment and that is all they truly support (which was one of the motivations behind the workbench development)

            Do you have a LINUX box to use? Alternatively, did you try the workbench again and check out the console messages? (see my replies to your other messages)

            Cheers,
            Matt

  • Bo Zhu

    Hi,

    I downloaded the latest one and my system is Centos 6.4. When I ran “Java -jar Workbench.jar”, I got an error

    UEA sRNA Workbench startup…

    Mar 07, 2014 5:42:32 PM org.apache.pdfbox.pdmodel.font.PDTrueTypeFont getawtFont

    INFO: Using font SansSerif.plain instead

    Mar 07, 2014 5:42:32 PM org.apache.pdfbox.pdmodel.font.PDTrueTypeFont getawtFont

    INFO: Using font SansSerif.bold instead

    Mar 07, 2014 5:42:32 PM org.apache.pdfbox.pdmodel.font.PDTrueTypeFont getawtFont

    INFO: Using font SansSerif.plain instead

    Exception in thread “AWT-EventQueue-0” java.lang.RuntimeException: java.lang.UnsatisfiedLinkError: Can’t load library: /home/zhubo/software/srna-workbenchV3.1/srna-workbench/lib/amd64/libglass.so

    at com.sun.javafx.tk.quantum.QuantumToolkit.startup(QuantumToolkit.java:284)

    at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:127)

    at javafx.embed.swing.JFXPanel.initFx(JFXPanel.java:182)

    at javafx.embed.swing.JFXPanel.(JFXPanel.java:199)

    at uk.ac.uea.cmp.srnaworkbench.swing.webbrowser.FXBrowser.(FXBrowser.java:29)

    at uk.ac.uea.cmp.srnaworkbench.startup.StartupOptionsLicence.createHTMLView(StartupOptionsLicence.java:594)

    at uk.ac.uea.cmp.srnaworkbench.startup.StartupOptionsLicence.checkOptionState(StartupOptionsLicence.java:549)

    at uk.ac.uea.cmp.srnaworkbench.startup.StartupOptionsLicence.nextStartupOption(StartupOptionsLicence.java:473)

    at uk.ac.uea.cmp.srnaworkbench.startup.StartupOptionsLicence.nextBtnActionPerformed(StartupOptionsLicence.java:579)

    at uk.ac.uea.cmp.srnaworkbench.startup.StartupOptionsLicence.access$200(StartupOptionsLicence.java:34)

    at uk.ac.uea.cmp.srnaworkbench.startup.StartupOptionsLicence$3.actionPerformed(StartupOptionsLicence.java:134)

    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)

    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)

    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)

    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)

    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)

    at java.awt.Component.processMouseEvent(Component.java:6505)

    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)

    at java.awt.Component.processEvent(Component.java:6270)

    at java.awt.Container.processEvent(Container.java:2229)

    at java.awt.Component.dispatchEventImpl(Component.java:4861)

    at java.awt.Container.dispatchEventImpl(Container.java:2287)

    at java.awt.Component.dispatchEvent(Component.java:4687)

    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)

    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)

    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)

    at java.awt.Container.dispatchEventImpl(Container.java:2273)

    at java.awt.Window.dispatchEventImpl(Window.java:2719)

    at java.awt.Component.dispatchEvent(Component.java:4687)

    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)

    at java.awt.EventQueue.access$200(EventQueue.java:103)

    at java.awt.EventQueue$3.run(EventQueue.java:694)

    at java.awt.EventQueue$3.run(EventQueue.java:692)

    at java.security.AccessController.doPrivileged(Native Method)

    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)

    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)

    at java.awt.EventQueue$4.run(EventQueue.java:708)

    at java.awt.EventQueue$4.run(EventQueue.java:706)

    at java.security.AccessController.doPrivileged(Native Method)

    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)

    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)

    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)

    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)

    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)

    at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)

    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)

    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)

    at java.awt.EventQueue.access$200(EventQueue.java:103)

    at java.awt.EventQueue$3.run(EventQueue.java:694)

    at java.awt.EventQueue$3.run(EventQueue.java:692)

    at java.security.AccessController.doPrivileged(Native Method)

    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)

    at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)

    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)

    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)

    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)

    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)

    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)

    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

    Caused by: java.lang.UnsatisfiedLinkError: Can’t load library: /home/zhubo/software/srna-workbenchV3.1/srna-workbench/lib/amd64/libglass.so

    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1854)

    at java.lang.Runtime.load0(Runtime.java:795)

    at java.lang.System.load(System.java:1062)

    at com.sun.glass.utils.NativeLibLoader.loadLibraryFullPath(NativeLibLoader.java:200)

    at com.sun.glass.utils.NativeLibLoader.loadLibraryInternal(NativeLibLoader.java:88)

    at com.sun.glass.utils.NativeLibLoader.loadLibrary(NativeLibLoader.java:31)

    at com.sun.glass.ui.Application.loadNativeLibrary(Application.java:74)

    at com.sun.glass.ui.Application.loadNativeLibrary(Application.java:81)

    at com.sun.glass.ui.gtk.GtkPlatformFactory$1.run(GtkPlatformFactory.java:28)

    at com.sun.glass.ui.gtk.GtkPlatformFactory$1.run(GtkPlatformFactory.java:25)

    at java.security.AccessController.doPrivileged(Native Method)

    at com.sun.glass.ui.gtk.GtkPlatformFactory.(GtkPlatformFactory.java:25)

    at java.lang.Class.forName0(Native Method)

    at java.lang.Class.forName(Class.java:190)

    at com.sun.glass.ui.PlatformFactory.getPlatformFactory(PlatformFactory.java:20)

    at com.sun.glass.ui.Application.Run(Application.java:104)

    at com.sun.javafx.tk.quantum.QuantumToolkit.startup(QuantumToolkit.java:274)

    … 58 more

    Any suggestions? Thanks My Java version is OK

    • The sRNA Workbench

      Hi,

      Can you enter java -version into the terminal for me and copy paste exactly what it reports back to you?

      Cheers,
      Matt

      • Bo Zhu

        Thanks for quick response

        the report is here

        java version “1.7.0_45”
        OpenJDK Runtime Environment (rhel-2.4.3.3.el6-x86_64 u45-b15)
        OpenJDK 64-Bit Server VM (build 24.45-b08, mixed mode)

        • The sRNA Workbench

          Hi Bo,

          I am afraid the software is not supported on the OpenJDK. It just does not seem to work as expected. Could you please install the latest version of the official Oracle Java and let me know if you still have issues?

          Best wishes,
          Matt

          • Bo Zhu

            Thanks. It’s working now!

            Bo

          • The sRNA Workbench

            Great 🙂 Let me know if you have any other questions

  • sanjay

    Hi ,
    I downloaded the linux version srna-workbenchV3.1_Linux and extracted it.
    However, when I tried to run it as following, I got error.

    java -jar Workbench.jar -tool mircat

    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)

    Could not find the main class: uk.ac.uea.cmp.srnaworkbench.Main. Program will exit.

    Java is loaded by default on our server and the version is java version “1.6.0_17”

    Thanks

    • The sRNA Workbench

      Hi,

      The latest version of the program requires the Oracle build of Java 1.7+

      Sorry the program should warn when an out of date version of Java is detected but perhaps it is not so reliable on Linux.

      I will look into why the warning was not shown!

      Cheers,
      Matt

  • Nitin

    Hi Matt, I looked for but could not find the manual for running the mirprof and Siloco on a command line. Can you please send me the link to the document that describes how to run these tools on a command line? I have 100s of samples to analyze and so I want to automate it. Also, can you please tell me which files I need to download in order to install the tool on my linux box?

    Thanks,
    Nitin

    • The sRNA Workbench

      Hi Nitin,

      The software is written in Java so will run on a Linux box as is (just choose the linux download as this contains no stub launchers, if you visit the sourceforge page on a Linux system it will automatically point you at the linux builds)

      To run any tool from the command line you can follow the instructions here:

      http://srna-workbench.cmp.uea.ac.uk/quick-start/

      miRProf will require miRBase files to be downloaded prior to execution. Examples for each parameter file used to control the tools execution can be found in your download directory in data/default_params (choose the tool that you want and modify the parameters in a text editor, any parameter you do not set will use a default value)

      I hope this helps, please let me know if you have any trouble getting the command line version to execute

      Cheers,
      Matt

  • Andrius

    this is a message I receive while trying to install “srna-workbenchV3.1” is damaged and can’t be opened. You should eject the disk image.” Mac OS 10.9.1. Any suggestions?

    • The sRNA Workbench

      Hi Andrius,

      I am not sure exactly what has caused that. I do not have that OS installed as yet (is it mavericks?) I am still on Lion at the moment! I will install a copy onto one of the machines here at the University and see if I can figure out why it did not work. Do you want me to send you a copy of the .app file rather than the .dmg and see if that works for you?

      Cheers,
      Matt

      • Andrius

        Hey Matt, yes, it is Mavericks.
        Lets try app file, but I think problem is the OS.
        krosingoveris@gmail.com

        Thanks,
        Andrius

        • The sRNA Workbench

          Hi Andrius,

          I have heard a few problems still exist with the OS so I was a little reluctant to install it but I think I have no choice because I need to test the software on it! The app file is a little large, I will upload it somewhere and email you a link. Hopefully it will just be the disk image that has caused the issue

          Cheers,
          Matt

          • The sRNA Workbench

            Hi Andrius,

            I have made some progress here. I installed Mountain Lion first and attempted to run the software and got what appears to be a similar damaged message.

            So I opened up the .app package (right click and show package contents) and attempted to fire the java program from there. It wouldn’t let me run because the default security settings on this OSX are to allow only verified publishers and app store downloads to run. So I had two choices, one was to change the security setting (in system preferences) or to just right click on the application and click open, then tell it to always allow this program to run.

            However, I still could not launch the application from the .app file. Turns out, the stub launcher also needs to have a permission set because it was downloaded from the internet and contains a partial apple signature. I have a solution, I need to repackage the program using a stub that does not contain any apple signature at all… I have done this but will not upload it today as I need to test it all out.

            For now, the solution will be to go to the .app file I sent you, show package contents, then go to resources/Java and hold ctrl and click on sRNAWorkbenchStartup.jar and select ‘open’

            Alternatively you can go to your security settings and allow any application to open (SystemPreferences/Security&privacy -> general -> Allow applications downloaded from Anywhere) and launch the application as normal.

            This is only on Mountain Lion but I am willing to bet it is the same on Mavericks to be honest. I will install that version of the OS later today and test it. Then I will upload the new stub launcher early next week.

            Thanks for pointing out the problem, let me know if this helps and you get the program to launch!

  • Pingback: UEA sRNA Workbench 3.0 - Analysing micro RNA and other small RNA data from High-Throughput Sequencing devices()

  • Tibor Nagy

    Can we download the source code?

    • Hi Tibor,

      As yet no but I may make the source open in the near future if enough people are interested.

      Cheers,
      Matt

  • Ben

    Hi Matt,
    I am now trying to use ta-si prediction tool in small rna workbench v2.5.0. It just works well with test data in tutorial, and shows no result with my own data, 2 GB solexa small rna data. So I check the output file in user dir, there is nothing in the patman file. However It looks right in patman outflie when just run patman in EXEfile dir with my data. How about your kind advice to dissolve it? The computer environment is centos6.3, 128G RAM. Thank you.

    • Hi Ben,

      Could you provide me with a small sample of the exact small RNA file you input into miRProf? You can send it to my email address:

      matthew.stocks@uea.ac.uk

      just the first few lines should be enough 🙂

      Cheers,
      Matt

  • Xi Wang

    I have downloaded the workbench V2.4.2 for Linux and tried to run the tool SiLoCo. However I got error messages looking like this:

    Exception in thread “AWT-EventQueue-0” java.lang.ArrayIndexOutOfBoundsException: 24
    at uk.ac.uea.cmp.srnaworkbench.tools.siloco.SiLoCoProcess$1.run(SiLoCoProcess.java:402)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
    Aug 27, 2012 2:42:00 PM uk.ac.uea.cmp.srnaworkbench.utils.WorkbenchLogger log
    SEVERE: WORKBENCH: SEQ ALIGN: Message: /ebio/abt6_projects/backup/solexa_tools/srna-workbench/srna-workbenchV2.4.2/User/temp/_3/combined_data.fa_filtered.fa.0.chunk.patman (No such file or directory);
    Stack Trace: java.io.FileInputStream.open(Native Method)
    java.io.FileInputStream.(FileInputStream.java:106)
    uk.ac.uea.cmp.srnaworkbench.utils.FileUtils.concatFiles(FileUtils.java:436)
    uk.ac.uea.cmp.srnaworkbench.utils.patman.PatmanRunner.process(PatmanRunner.java:145)
    uk.ac.uea.cmp.srnaworkbench.tools.RunnableTool.run(RunnableTool.java:339)
    java.lang.Thread.run(Thread.java:662)

    And then I got no results out of it, although it showed “completed successfully”. Any idea what is wrong?

    • just approved this comment and deleted the other one. For anyone interested it was just due to missing dependancies on Ubuntu Linux (most likely 32bit libs and popt, if you require further information please feel free to contact me).

      I think I will look into compiling a 64bit version of patman to counteract the missing 32bit libs. This, however, will not stop people running into problems if they have not installed popt on their linux systems. Eventually we will include further sequence alignment programs that will hopefully give another avenue for people to go down if they run into this issue and do not have root privileges on their system

  • Cam

    Hi To-who-may-be-concern,

    I have downloaded the latest version and I have trouble opening the java in window vista. Please advise.

    I deeply appreciate your reply and thank you for your kind attention.

    • Hi,

      Can you be more specific about the problem? Did you fully extract the workbench directory? Did you launch the program from the sRNAWorkbenchStartup.jar (by double clicking)?

      If you wish to conduct the conversation in private please feel free to email me at matthew.stocks@uea.ac.uk or just reply here.

      Best wishes,
      Matthew

      • Hi again,

        I have just managed to find a machine running Vista (most of our MS computers are using Windows 7 at the moment).

        I also had a little bit of trouble getting the program to launch. To solve it, I first had to make sure the program was located on a local directory (not network) with no spaces in the path. Then I had to actually launch the program from the command line rather than double clicking. Vista seems to want many yes/no boxes pressed before it will allow the program to launch (firewall etc). In addition, as this machine was a “public” lab computer (i.e. used by students) I believe some security features were preventing the startup program from launching the main Workbench program. When the CMP support team return from their morning meetings I will discuss it with them. Chances are this will not affect W7 users (as I mainly test the windows build on this OS)

        For now, I would first ensure you have no spaces in the path to the workbench. Then open a command window in the directory (this can sometimes be done using shift+right click and “open command window here”) failing that, open the all programs list, type ‘cmd’ into the run/search box. Then type ‘cd’ followed by the path to the workbench (ctrl c to copy the path from the windows explorer and right click and ‘paste’ to place it into the command window) then type:

        java -jar sRNAWorkbenchStartup.jar

        to launch the program. Answer yes to all the questions about windows firewall blocking certain features of the program.

        Let me know if this is unclear. I will reply again when I have a little more information on the Vista security possibly blocking the program from double click.

  • Kenlee Nakasugi

    Hi,

    I’ve just downloaded v2.4, and started up Workbench.jar as per:
    java -Xmx10g -Xms10g -jar Workbench.jar.

    I’ve loaded miRCat, but when I try and load the sRNA and genome files in the ‘new project’ window, the ‘OK’ button doesn’t seem to work when I select the filter Input, but it does load when that checkbox is off. I don’t think this happened in previous version, unless it tries and do the filtering straight away in this new version and is taking time filtering and loading.

    Not sure if this is a bug or supposed to behave this way, but I can’t set it to do filtering on the data. There seems to be a point exception (see below). I’m using Ubuntu 10.04 with 16Gb RAM, and the reference genome is 2.3Gb while the sRNA read data is 500MB.

    Could you confirm if it just needs time loading when the ‘filter input’ option is checked?

    Many thanks,
    Ken

    ################
    This appears in the bash window:

    MBS: removed stack trace from post as it is rather long

    • Hi Ken,

      Further to my email last week I have identified the problem and will be releasing a fix along with the next version of the workbench (which will hopefully be quite soon but there are some other small issues I must address before it is ready, however, this may end up pushing the release forward a little)

      For now as we discussed you can use the Filter tool aside from miRCat and use the History Browser to retrieve your filtered data set.

      Thanks very much for pointing this out, as usual, this kind of feedback is a great help to me with this project!

      Matt

      • For anyone following this bug, it is fixed in Version 2.4.2

        Thanks,
        Matthew

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