Applying Matlab variables in a UNIX command

I am building a MATLAB script to generate many input files with unique file names, then to feed these files to a program that can only be run from the command line (UNIX, I'm on a Mac). One of my final barriers is to be able to use MATLAB variables in the UNIX command line. This is a very basic example, but for instance if I execute the following code:

folderName = test;
unix('cd /path; mkdir folderName')

the folder is created with the name "folderName" rather than test, whereas I was hoping for the path /path/test to be created. Any ideas?

Thank you very much!

Answer 1

[Thorsten]

You can create the folder in Matlab as follows:

 path = '/User/foobar/Matlab/xxx';
 folder = 'test';
 mkdir(fullfile(path, folder))

[Kevin]

Thank you for your reply. It's clear to me that I did a poor job in asking this question, but it's important that I run in the UNIX environment.

I have a program that only runs from the command line, and I'm giving it input variables in the filename used in the command that are variables in the Matlab script. If I use UNIX, the command would look like

Program filename_var1_var2.txt

Etc, etc. Any ideas? Thank you.

[Thorsten]

You have to write the text file filename_var1_var2.txt from Matlab, and then call your program from the command line or from Matlab using system. What's the format of filename_var1_var2.txt? Do you have problems generating this file from Matlab? Have a look at Walter's answer that shows the principle way of how to do it.

Answer 2

[Walter Roberson]

folderName = 'test';
unix( sprintf('cd /path; mkdir ''%s''', folderName) )

If you want to live dangerously:

folderName = 'test';
unix( ['cd /path; mkdir ', folderName] )

which would lead you to endless fun if the folderName contained any shell special characters.

[Walter Roberson]

for K = 1 : 20
   %generate temporary file names
   this_infile = tempname();
   this_outfile = tempname();

     %create some input data
     fid = fopen(this_infile, 'w');
     fprintf(fid, '%f ', rand(1,10) );
     fprintf(fid, '\n');
     fclose(fid);

     %build the command
     cmd = sprintf('YourProgram ''%s'' >> ''%s''', this_infile, this_outfile);

     %run the command
     [status, cmd_output] = system(cmd);

     %read the output file
     fid = fopen(this_outfile, 'r');
     results = fscanf(fid, '%f', 1);
     fclose(fid);
     fprintf('Run #%K responded with: %f\n', results);

     %get rid of the files
     delete(this_infile);
     delete(this_outfile);
   end

[Kevin]

Hi Walter,

Thank you for the reply. I've tried to implement your suggestion but have ran in to more issues with my program. I am trying to use a program called SIMPSON from a variable directory as determined in the first unix command. When I run the following code:

function s=SimpExecute(simpsonInput)
   cmd = 'cd /Users/kevin/Desktop/Sims/PulseSims;simpson simpsonInput';
   [status,cmd_output] = unix(cmd)
end

I get the results:

status = 127
cmd_output = /bin/bash: simpson: command not found

Strangely, when I run the identical command in the Terminal command line, SIMPSON runs perfectly. Perhaps the path is misset? However when I type

whereis simpson

in Terminal, it outputs no results.

I have re-run the top code, but instead of trying to run SIMPSON I asked it to echo the path of the environment after changing directories

function s=SimpExecute(simpsonInput)
   cmd = 'cd Desktop/Sims/PulseSims;echo $PATH';
   [status,cmd_output] = unix(cmd)
end

and receive this is output:

status =

     0

cmd_output =

/usr/bin:/bin:/usr/sbin:/sbin

I'm at a loss. Do you have any suggestions? Thank you in advance for your help. Cheers.

[Walter Roberson]

Your PATH does not include your current directory. You could add that to the PATH, or you could change your command to

cmd = 'cd /Users/kevin/Desktop/Sims/PulseSims;./simpson simpsonInput';

Something in your program must have reset your PATH, or else you have started MATLAB in an odd way. For me on OS-X, starting by clicking the icon in the dock, I get

/Applications/MATLAB_R2014a.app/sys/java/jre/maci64/jre/bin:/Library/Frameworks/Maple.framework/Versions/2016/bin.APPLE_UNIVERSAL_OSX:/Library/Frameworks/Maple.framework/Versions/2016/jre.APPLE_UNIVERSAL_OSX/bin/:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MATLAB_R2014a.app/bin:/Applications/MATLAB_R2014a.app/bin/maci:/Applications/MATLAB_R2014a.app/sys/os/maci:/Applications/MATLAB_R2014a.app/bin/maci64:/Applications/MATLAB_R2014a.app/sys/os/maci64

If you are starting MATLAB from the command line on a Linux system then you would be invoking a shell script named "matlab" which should set the PATH and then invoke the MATLAB executable. It is not impossible that someone has mangled that script.

The only other reason I can think of that your PATH might be like that is if someone has changed the actual MATLAB executable to be suid or sguid : in such a case in order to prevent security problems, the operating system would automatically change to a restricted PATH very similar to the one you are seeing, ignoring any environment variables.

[Kevin]

Walter,

Thank you again for your reply. I tried your suggestions, and while they did not work exactly, your comment got me thinking. In the end I only had to add a bit to PATH:

PATH=$PATH:/bin:/usr/local/bin

and it was able to find the command simpson. Thanks so much for your help and inspiration!