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Running other scripts from Bash shell


I am running Cygwin on a Windows 2000 machine. I also have GNU Octave 2.1.50
(very similar to Matlab) installed. Cygwin is a component of the GNU Octave
2.1.50 build, but I have installed Cygwin seperately as well. As a result of
this, my octave and cygwin programs do not run together and have different
root directories. Will this cause any trouble calling an Octave script from
a bash script under Cygwin? My root directories are C:/cygwin and C:/Program
Files/GNU Octave 2.1.50/

I would like a bash script (scheduled with cron) that is located in
C:/cygwin/bin to call some Octave scripts that I have in C:/Program
Files/GNU Octave 2.1.50/octave_files/

What is the best way of running scripts that are not associated with the
Cygwin platform? Any advice would be greatly appreciated.

Thanks

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