How to run a Perl script

Question

[Javad]

Hello,

I do not have any experience in Perl scripting. I have a Perl script that is specifically designed to convert GFF/GTF formatted files to BED files (here is the script). Can any help me to run this script for format conversion. It would be grate if I can have a step by step guide about how to run it because I am completely unfamiliar with it,

Thanks a lot

[Satyajeet Khare]

The script is a part of ea-utils package. Just check the readme and build instructions.

Answer 1

[Jean-Karim Heriche]

Learn perl.

Answer 2

[Samarth Kulshrestha]

Assuming that Perl is installed on your machine: You can run any Perl program using the syntax:

perl yourprogram.pl

Hope this help

[Javad]

Thanks, But how I can define the input and output file?

[Medhat]

depending on you perl script. how the script accept the input and output files?! so beside learning perl as Jean-Karim Heriche said you need also to read the documentation about the perl script you will use.

[Samarth Kulshrestha]

I can find out that your script is a part of a package called "ea-utils". Below is the link to the package:

Step1: Just download the package from the given link below. https://github.com/ExpressionAnalysis/ea-utils

Step2: Unzip the package

Step3: Just compile and install it using the instructions mentioned in the tutorial: https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/Compiling.md

After you install it on your machine, you need to check the required parameters of the script

I assume that you have Linux installed on your machine.