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  1. Jalview
  2. JAL-3523

OSX - Current working directory not preserved when Jalview.app launched with parameters from command line

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    Details

    • Type: Bug
    • Status: Ready for testing
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.11.0, 2.11.1, 2.11.1.0, 2.11.1.1
    • Fix Version/s: 2.11.2
    • Component/s: launcher
    • Labels:
    • Environment:
      OSX 10.3.6 (and higher)
    • Urgency:
      Urgent

      Description

      Files written by Jalview appear in the Jalview.app directory when it is launched in batch mode via:

      open -a /Applications/Jalview.app open /../examples/uniref50.fa png uniref50.png

      or

      open /Applications/Jalview.app --args open /../examples/uniref50.fa png uniref50.png

      According to [~gmungoc] in JAL-3386 (https://issues.jalview.org/browse/JAL-3386?focusedCommentId=22318&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-22318) any files written appear at /Applications/Jalview.app/Contents/Resources/app

      This behaviour is cumbersome, because full paths to input data need to be specified, and could potentially result in a Jalview corrupting its own installation by overwriting files during execution of a command line.

      For existing users calling Jalview's command line operations in this way, full paths for output files should be used.

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              Assignee:
              soares Ben Soares
              Reporter:
              jprocter Jim Procter
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                Dates

                Created:
                Updated: