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[SCIRUN-USERS] Default path settings when running SCIRun in bash


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  • From: "Doshi, Ashish" <ashishdoshi@seas.wustl.edu>
  • To: "scirun-users@sci.utah.edu" <scirun-users@sci.utah.edu>
  • Subject: [SCIRUN-USERS] Default path settings when running SCIRun in bash
  • Date: Mon, 5 Jan 2015 17:27:56 +0000
  • Accept-language: en-US
Dear SCIRun Users,

Happy New Year to all! I hope everyone has an enjoyable and productive 2015.

I’ve encountered a quirk in the way SCIRun reads the path settings of the
shell launching SCIRun.

I recently switched over from running SCIRun 4.7 on a Windows 64-bit machine
to running 4.7 on a Mac running OS X 10.10 (Yosemite). I use the
InterfaceWithMatlab module quite a bit, and when I was using Windows, I
modified the path variable to point to MATLAB’s directory. With OS X, I just
added the path to MATLAB in the .bashrc file in my home directory. When I
launch SCIRun using the OS X GUI (i.e. double-clicking on the SCIRun
application icon in the Applications folder), the X11 window that pops up
shows my path as follows: PATH=/usr/bin:/bin:/usr/sbin:/sbin. The
InterfaceWithMATLAB module is unable to run MATLAB.

However, if I open X11 and run SCIRun from there using the command,
"/Applications/SCIRun/SCIRun.app/Contents/MacOS/SCIRun", the path reflects
the MATLAB path that I included in my .bashrc file:
PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/X11R6/bin:/opt/X11/bin:/Applications/MATLAB_R2014b.app/bin:/Applications/MATLAB_R2014b.app/bin/maci64:/Applications/MATLAB_R2014b.app/.
Opening SCIRun this way enables me to use the InterfaceWithMATLAB module.

This is not a major problem as I can easily run SCIRun from X11. However,
I’m very curious as to why the path would be different with these two
methods. When double-clicking on the SCIRun app icon, what does SCIRun use
as a default .bashrc file? Why would it overlook the .bashrc file in my home
directory? I’ve tried placing my .bashrc file in the root directory, but it
shouldn’t really make a difference as the default bashrc file should be
looking system-wide for any user-modified .bashrc file.

Ashish Doshi, MD, PhD
Post-doctoral Fellow
Department of Biomedical Engineering
Washington University in St. Louis
  • [SCIRUN-USERS] Default path settings when running SCIRun in bash, Doshi, Ashish, 01/05/2015

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