Help with troubleshooting perl script

Question

[plath.jar]

Hey guys! I am using a script I found here :

However, I keep getting this error

Can't exec "/path/to/folder/Peak_Calling_for_CATaDa-master/sub_programs/RPM_normalise_and_average.pl": No such file or directory at /path/to/folder/Peak_Calling_for_CATaDa-master/CATaDa_analysis_pipeline.pl line 57, <STDIN> line 3

I have confirmed that RPM_normalise_and_average.pl is at location /path/to/folder/Peak_Calling_for_CATaDa-master/sub_programs/. I have also confirmed that the script is executable.

I'm new to this. Could someone please tell me what I am missing?

Answer 1

[Mensur Dlakic]

First of all, the error says:

path/to/folder/Peak_Calling_for_CATaDa-master/CATaDa_analysis_pipeline.pl

That's not the same as /path ... Second, it is almost impossible that you have an executable in that position (/path/to/folder/ ...) because such a directory doesn't exist on most computers. In that line a real directory location should be entered, and then you make sure the script is in the same location.

[plath.jar]

Thanks for pointing that out! However, the script actually specifies the path to the directory with the executable using

Use Cwd; my $dir = getcwd;

and then uses

system("$dir/sub_programs/RPM_normalise_and_average.pl", "$exp_name", "$paths", "$rep_num");

This gives path/to/folder/Peak_Calling_for_CATaDa-master/sub_programs/... etc. I meant to say that the .pl executable is in that folder. Do you think that sounds correct?