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  1. Jalview
  2. JAL-764

tree passed via command line not written to jalview project when in headless mode

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Command Line Interface, gui
    • Labels:
      None

      Description


      First noticed by Julien Roux:
      > I am trying to create a jalview file (.jar) including an amino-acid alignment, the associated tree and some annotations.
      > To do this, I want to use the command line. I tried:

      java -Djava.ext.dirs=/Applications/Jalview/lib -cp /Applications/Jalview/Jalview.jar jalview.bin.Jalview -open my_aln.fas -colour ZAPPO -annotations my_annot.jalview -tree my_tree.nwk -jalview test.jar

      > This works fine and creates the test.jar file correctly. However, when I add the -nodisplay option to do this without User Interface,
      > the file test.jar does not include the associated tree. Is this a bug or I am doing something wrong?

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              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
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                Created:
                Updated: