[Mesquitelist] running MESQUITE from the command line - specifying a project file to open

[Wayne Maddison]

Open up Run_Mesquite_OSX.command in a text editor; you'll see a line like

java  -Xmx500M -Xss2m -Djava.library.path=lib -cp "$dir" mesquite.Mesquite

Basically, you'll enter something like that in Terminal.

First, find the path to Mesquite_Folder.  Suppose it's in 
/Applications.  Second, find the path to your data file.  Suppose 
it's on your user Desktop, i.e. 
"/Users/Budd/Desktop/myMesquiteNexusProject.nxs"

Now open Terminal.  Enter the command:

java  -Xmx500M -Xss2m -Djava.library.path=lib -cp 
/Applications/Mesquite_Folder mesquite.Mesquite 
'/Users/Budd/Desktop/myMesquiteNexusProject.nxs'


Alternatively, open up Mesquite without a file, then, from the 
command line, request a file to be opened:

openfile '/Users/Budd/Desktop/myMesquiteNexusProject.nxs'

If you don't want the windows to appear, include -w in the arguments:

java  -Xmx500M -Xss2m -Djava.library.path=lib -cp 
/Applications/Mesquite_Folder mesquite.Mesquite 
'/Users/Budd/Desktop/myMesquiteNexusProject.nxs' -w

You could also use the headless version.

A hint: when operating Mesquite by the command line, you can find the 
list of high level commands by typing "help".  Even in the headless 
version there is a sense of "windows" existing, which you can find 
and command using sw and jw.

You can find the list of commands specific to the object being 
commanded by typing ?.

Wayne


At 10:25 AM +0200 29.4.2009, Aidan Budd wrote:
>Hi again, MESQUITEers
>
>Rather than tacking this on the end of my previous mail, thought it might
>be better to give it a separate thread...
>
>I'd like to be able, on my OSX machine, to run/execute MESQUITE from the
>command line in a way that specifies, via the command-line invocation, a
>NEXUS file to open in MESQUITE.
>
>I can start MESQUITE no problem from the command line, simply invoking the
>Run_Mesquite_OSX.command script
>
>However, knowing almost exactly nothing about java, I haven't been able to
>work out how to alter the java invocation to specify a MESQUITE
>NEXUS-format file to open on starting MESQUITE so that I can do something
>like:
>
>Run_Mesquite_OSX.command myMesquiteNexusProject.nxs
>
>so that MESQUITE will start, and then open "myMesquiteNexusProject.nxs"
>
>Any suggestions on how to do this would be much appreciated - or, of
>course, the advice to stop trying to do it as it's not appropriate/doesn't
>make sense!
>
>Thanks
>
>Aidan
>
>--
>----------------------------------------------------------------------
>Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
>EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
>Meyerhofstr. 1, 69117 Heidelberg, Germany
>
>http://www.embl-heidelberg.de/~budd/
>http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
>
>_______________________________________________
>Mesquitelist mailing list
>Mesquitelist at mesquiteproject.org
>http://mesquiteproject.org/mailman/listinfo/mesquitelist


-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416

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