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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Wed May 21 18:27:24 EDT 2008


You're using '>out.aln.pfam' as the full path for the output file. Most 
probably, the file is being produced but in the same location where the 
CGI script lives. Check inside the same directory where you installed 
your script.

Mauricio.

vdar at yorku.ca wrote:
> 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"
> 
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM


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