在CGI脚本中运行perl脚本

Question

I am a newbie in Bioinformatics but I know perl scripting. I've written few scripts for parsing pdb files(protein crystal structure files). Now I want to run these in a web server. I have apache2 installed in my ubuntu. I have read something about the CGI and is in /usr/lib/cgi-bin/ in local web server. I need to have all my perl scripts in that directory. These scripts takes input from command line ex: perl contacts.pl pdbFile.pdb .

Now how can I run these scripts inside a perl CGI script so that the CGI script throws html page on the fly and asks for user input (this includes PHP I guess). At the end I should have a html page able to run my perl script ( contacts.pl ) upon user input.

If its not possible to run my perl script in html web page, what is the other alternative?

Any help will be greatly appreciated.

Answer 1

I don't think I'd run everything through CGI. If I were you, I'd look at using a perl web framework to handle generating the webpages and (presumably) uploading files, and then call your existing code to parse the pdb files and get whatever you're interested in.

Some popular frameworks:

• Mojolicious: http://mojolicio.us/
• Dancer: http://perldancer.org/

As for running the webserver, they should have deployment guides with instructions for apache. Or use another webserver like starman that can run perl webapps easily.

Answer 2

For a start you can get basic ideas from below links :

Perl/CGI script with Apache2

CGI script calling a perl script

First Perl CGI script