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  • MEGAN command line without X11?

    Hi all,

    I just install Mac OS 10.8 and it turns out that X11 is no longer part of the install. I have been running MEGAN via X11 in the past (command line), but I'm wondering if there is a way to run it without X11 requirements?

    I launch it in 'non-GUI' mode, but apparently it still needs a GUI:

    Code:
    ./MEGAN +w +s +g -x <commands>
    I have tried various combinations of +g, +w, +s, etc., but it always fails to run with the following (X11 requirement) error:

    Code:
    No X11 DISPLAY variable was set, but this program performed an operation which requires it.
    java.awt.HeadlessException
    Thanks very much in advance

  • #2
    This might work : http://xquartz.macosforge.org/landing/
    The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5

    Comment


    • #3
      Originally posted by kga1978 View Post
      Hi all,

      I just install Mac OS 10.8 and it turns out that X11 is no longer part of the install. I have been running MEGAN via X11 in the past (command line), but I'm wondering if there is a way to run it without X11 requirements?

      I launch it in 'non-GUI' mode, but apparently it still needs a GUI:

      Code:
      ./MEGAN +w +s +g -x <commands>
      I have tried various combinations of +g, +w, +s, etc., but it always fails to run with the following (X11 requirement) error:

      Code:
      No X11 DISPLAY variable was set, but this program performed an operation which requires it.
      java.awt.HeadlessException
      Thanks very much in advance

      If you are not trying to submit a PBS job for megan, you can try the following commands:

      ./MEGAN +g false -x <commands>

      Here is my terminal:

      $ MEGAN +g false -x "import blastfile=test.blastx.out meganfile=test.blastx.rma"
      Picked up _JAVA_OPTIONS: -Xmx1365333k
      MEGAN (version 4.68.1, built 8 Jun 2012)
      Message - License type: Academic
      Licensed to user: deleted
      Academic institution: deleted
      Email: deleted

      File name: ncbi.tre
      Loading mapping file: ncbi.map
      Load mapping:
      ...

      Comment

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