[Bioperl-l] Bio-perl and webpages?

Paulo Almeida palmeida at igc.gulbenkian.pt
Tue Jul 19 10:31:05 EDT 2005

Hi Elena,

If you already have your scripts in Perl it would probably be best to 
use the Perl CGI module, instead of php ( you can find it at 
http://search.cpan.org/dist/CGI.pm/ ). You can adapt the input so it is 
read from a web form and change the print commands to print html.

Incidentally, I'm not sure this is appropriate for the list, but since 
I'm on the subject... I tried to adapt a script to run on the Web; I 
wanted to use Taint mode but I got an error saying that something on the 
Clustal module of BioPerl was using an unsafe variable:

Insecure $ENV{PATH} while running with -T switch at 
/usr/local/share/perl/5.8.4/Bio/Tools/Run/Alignment/Clustalw.pm line 
556, <GEN0> line 2.

I wouldn't mind hardcoding the path of Clustal, but I couldn't figure 
out a way to do it, or to untaint the variable. Can anyone help?


Elena Grassi wrote:

>I've got a bunch of scripts (ok, it should be a complete program, but
>that's not the point now...) written in perl (written with other people
>not that much object-oriented) and now I need to make them work through
>a website.
>My first idea is to use a little bit of dirty php, my second one is to
>translate perl in php (I have to admit that I'd prefer not to use this
>idea...), the third one involves bioperl: if I decide to try to re-write
>the scripts with bioperl is there any suitable and fast tool to put them
>into an html based structure?
>Sorry for the nearly OT question,

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