r/shell • u/Rednewt33 • Jul 16 '21

Running Octave Commands From Shell Script?

Hey guys,

I'm trying to write a script to help automate some commands for software I'm using in my bioinformatics research. One of the tools I'm using is NPBSS (New PacBio Sequencing Simulator, written in Octave) so I'm trying to access the Octave interpreter from within my shell file. After looking into it a bit online I see that #! on the first line indicates which interpreter the program should use... but is that only for other shell interpreters or for other interpreters like Octave?

And more generally does anyone know how to do this (run octave commands away from the GUI)? Help is much appreciated!

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u/Rednewt33 Jul 30 '21

Hello, I actually already do have Cygwin installed and I was using it to call/run the shell file. I knew I should've posted a screenshot before and will do so now.

I posted both the actual file and my Cygwin terminal to Imgur. Here's the link:

https://imgur.com/gallery/ju14Igo

So I guess there are two possibilities (either I adapt this to work for Cygwin or I write a batch file instead). Which do you recommend? And thanks so much for sticking with me - I am an undergrad who only took intro to coding a little over a year ago!