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I would like to run external command from Mathematica. For this I need to have bash environment configured via reading the content of ${HOME}/.bashrc file. When I execute the following code in Mathematica notebook

ReadList["!echo $PATH", String]

the content of PATH variable is not set as it is in ${HOME}/.bashrc. The same happens when I explicitly load bash configuration file

ReadList["!source ${HOME}/.bashrc; echo $PATH", String]

(strictly speaking the above command makes no effect!). So the question is: is it possible to load the configuration stored in .bashrc file in Mathematica external call under the Linux system (of course without explicitly setting e.g. mentioned PATH variable is not a solution for me)?

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  • $\begingroup$ try ReadList["!printenv",String] start by figuring aout what shell is running and what environment is avaialable. $\endgroup$
    – george2079
    Commented Dec 28, 2013 at 13:45
  • $\begingroup$ Why not use Run? $\endgroup$
    – Mike Honeychurch
    Commented Dec 28, 2013 at 22:50
  • $\begingroup$ Played with this a bit: you can reveal the actual shell with this: Readlist["!/bin/ps -p $$"] -- In my case I've got the bourne shell /bin/sh. printenv incorrectly shows the SHELL variable inherited from the shell used to invoke mathematica. So.. make shure your bashrc doesnt do anything incompatable with plain /bin/sh .. $\endgroup$
    – george2079
    Commented Dec 30, 2013 at 19:18
  • $\begingroup$ I don't understand the question. ReadList["!echo $PATH", String] gives me {"/usr/bin:/bin:/usr/sbin:/sbin"} which is expected since it did not read the contents of my bashrc file. If I do ReadList["!source $HOME/.bash_profile; echo $PATH", String] then I get all of the path that I have set up in there. $\endgroup$
    – jmlopez
    Commented Jan 2, 2014 at 1:43
  • $\begingroup$ As I have stated in the question ReadList["!source $HOME/.bashrc; echo $PATH", String] does not take any effect for me. $\endgroup$
    – mmal
    Commented Mar 9, 2014 at 11:36

1 Answer 1

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The solution for me is to start the Mathematica form a terminal, instead of Gnome launcher. Then the bash environment, when ReadList is executed, will be inherited from the shell itself.

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