Help with troubleshooting perl script
1
0
Entering edit mode
11 months ago
plath.jar • 0

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?

CATaDa • 421 views
ADD COMMENT
1
Entering edit mode
11 months ago
Mensur Dlakic ★ 28k

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.

ADD COMMENT
0
Entering edit mode

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?

ADD REPLY

Login before adding your answer.

Traffic: 1739 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6