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I have a very basic question. I have a shell file test.sh that prints let's say Yeah to a file called output.txt:

#!/bin/sh

echo "Yeah" > output.txt

I am running the Run command from the notebook:

Run["sh test.sh"]

But it is not creating the file output.txt. Can anyone tell me please what is going wrong?

Martin Ender
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Sayak
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    It works for me, are you looking in the right directory? When I run it Run["sh test.sh"] I get an output 0, and the output.txt shows up in the same directory. – Jason B. Mar 08 '16 at 16:21
  • Thank you Jason but it is a little strange. I am getting an output 0 only when I specify the entire path to test.sh (though both the notebook and test.sh are in the same directory). But even then I do not see output.txt in the same directory. So Run["sh /Users/sxm016/Documents/Alignment/Alignment_ras_sos/March_
    2016_ras_Gauss_multivariate/Bistable_traj/test.sh"] gives me an output 0 but no file named output.txt in the same directory     – Sayak Mar 08 '16 at 16:28
  • That is strange. What is the output from Directory[]? Perhaps the output.txt file is going somewhere in Mathematica's path? – Jason B. Mar 08 '16 at 16:32
  • Thank you so much. That is exactly what is happening. When I typed Directory[] it showed me the path to my home not the current directory. Thank you. Can you please tell me how to change the mathematica path ? – Sayak Mar 08 '16 at 16:37
  • you want SetDirectory[]. I actually have a line in my /home/jason/.Mathematica/Kernel/init.m file to say SetDirectory["~/Documents/Mathematica"]; so that I always start in that directory – Jason B. Mar 08 '16 at 16:39
  • Thank you Jason. I really appreciate your help. It works now – Sayak Mar 08 '16 at 16:43
  • @JasonB, Please repost your comment as an answer, so the Q/A makes sense and can be referenced. –  Mar 09 '16 at 14:54

1 Answers1

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The issue here is that when Mathematica executes an external system command, at least on Linux, it does so from the current directory. You can verify this via

Directory[]
Run["! echo $PWD > file.txt"];
FilePrint["file.txt"]

enter image description here

which is my default working directory. I actually have a line in my

/home/jason/.Mathematica/Kernel/init.m

file that says SetDirectory["~/Documents/Mathematica"]; so that I always start in that directory.

Jason B.
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