Using bash shell inside Matlab

Question

I'm trying to put a large set of bash commands into a matlab script and manage my variables (like file paths, parameters etc) from there. It is also needed because this workflow requires manual intervention at certain steps and I would like to use the step debugger for this.

The problem is, I don't understand how matlab interfaces with bash shell. I can't do system('source .bash_profile') to define my bash variables. Similarly I can't define them by hand and read them either, e.g. system('export var=somepath') and then system('echo $var') returns nothing.

What is the correct way of defining variables in bash inside matlab's command window? How can I construct a workflow of commands which will use the variables I defined as well as those in my .bash_profile?

Answer 1

If all you need to do is set environment variables, do this in MATLAB:

>> setenv('var','somepath')
>> system('echo $var')

Answer 2

Invoke Bash as a login shell to get your ~/.bash_profile sourced and use the -c option to execute a group of shell commands in one go.

# in Terminal.app
man bash | less -p 'the --login option'
man bash | less -p '-c string'
echo 'export profilevar=myProfileVar' >> ~/.bash_profile

# test in Terminal.app
/bin/bash --login -c '
echo "$0"
echo "$3"
echo "$@"
export var=somepath
echo "$var"
echo "$profilevar"
ps
export | nl
' zero 1 2 3 4 5


# in Matlab
cmd=sprintf('/bin/bash --login -c ''echo "$profilevar"; ps''');
[r,s]=system(cmd);
disp(s);