The small RNA Workbench Version 4.2.1 ALPHA

The small RNA Workbench Version 4.2.1 ALPHA: Released: 23/06/2016

This release is the next Alpha test for the latest version of the workbench, Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle

Download

General HotFix

  1. Added the 64bit binary for GhostScript LINUX build
  • The sRNA Workbench

    Hi Ram,

    Sorry for the delay, I am actually on leave this week so havent had a lot of time to look at support requests.

    I wasnt aware java 9 was available but I will download it when I return and test it all out. I would say though, that command is for using miRCat from the command line but also is using the startup jar rather than the software itself. If you wish to use the tool from the GUI simply type:

    java -Xms10g -Xmx10g -jar Workbench.jar

    to start the software with 10GB of RAM assigned to the VM, then open the menu and choose “show version 3.2” to get access to tools like PAREsnip etc. Where you going to use PAREsnip from the GUI or command line?

    Cheers,
    Matt

    • ram krishna shrestha

      Hi Matt
      I was able startup workbench after I installed java version 1.8 and sourced it. I was trying to find if the sequence reads contain any sRNA sequences by mapping the reads to refseq. The command was just a test to startup the workbench. Thanks a lot.
      Ram

      • The sRNA Workbench

        Hi Ram,

        no problem. I had a look around and it seems java 9 is only early release from the OpenJDK which we dont officially support as I dont have time to test it out! If you come into any other issues then give the Oracle build a go or let me know if there is anything else I can help with!

        Cheers,
        Matt

  • ram krishna shrestha

    sRNA Workbench (latest version)gets stuck while loading “PARESnip”. I got macbook pro El Capita with 16gb RAM and 2.3GHz i5 processors. The java is version 9. Any idea how I can start it?

    • The sRNA Workbench

      Hi Ram,

      Did you see my previous reply?

      Cheers,
      Matt

  • Túlio Campos

    Guys, what is the Java version to be used with this? I’m facing different issues with different Java versions and the same data. The exceptions are not informative.. Also please all add some “test data” to the package, so we know whether it’s a file format problem. Cheers!

    • The sRNA Workbench

      Hi,

      the java version must be version 8 or above of the Oracle JDK (it is untested with the open version)

      There is some test data in the download site on sourceforge listed as Tutorial Data and instructions on how to use it can be found in each video. The web page with the tutorial video references each file that is required from the tutorial data.

      Let me know if I can be any more help,

      Best wishes,
      Matt