[Bioperl-l] I can't access clustalw from my cgi perl program...

vdar at yorku.ca vdar at yorku.ca
Wed May 21 18:12:07 EDT 2008


ok thanks, its not giving me any error now, but its not doing anything too, the
following code works from commandline but not from my cgi script. I have added
the path to bioperl and have tried everything else that I could find...

        my  $in  = Bio::AlignIO->new(-file   => $inputfilename ,
				-format => 'fasta');
	my $out = Bio::AlignIO->new(-file   => ">out.aln.pfam" ,
				-format => 'pfam');



	while ( my $aln1 = $in->next_aln() ) {
		$out->write_aln($aln1);
	}


output file is not produced. what should I do?

thanks
nisa


Quoting Sendu Bala <bix at sendu.me.uk>:

> vdar at yorku.ca wrote:
> > How can I find where bioperl is installed?
>
> You already know where it's installed. See below.
>
>
> > Quoting Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>:
> >
> >> Hi Nisa,
> >>
> >> CGI scripts are generally run by a different user than you, and which
> >> user (e.g. apache, nobody) will depend on the platform you're running
> >> the script on, thus the environment variables you currently have for
> >> your login shell are not being inherited to the web interface. The best
> >> workaround for this is to add a 'use lib' pragma at the top of your CGI
> >> script:
> >>
> >> use lib '/path/to/your/bioperl/installation/';
> [...]
> >> vdar at yorku.ca wrote:
> >>> export PERL5LIB="/opt/rocks/lib/perl5/site_perl/5.8.8"
>




More information about the Bioperl-l mailing list