[Bioperl-l] bioperl and Bio::Factory::EMBOSS via cgi...permissionproblems?

[Tobias]

Brian, Rob,

thanks. that was indeed what i was waiting for! BUT: unfortunately it 
seems that with the new classes it is not possible to get the cut sites 
of a single enzyme but the fragments (which are of course internally 
calculated from the cut sites). second: my test digest with a 
non-palindromic cutter (BsaI) gave a wrong result.
Seems I have to digest "manually" ... or wait for the stable release?

thanks anyway
Tobias



Am Montag, 03.11.03 um 15:21 Uhr schrieb Brian Osborne:

> Tobias,
>
>> I have to run a restriction analysis through EMBOSS restrict (as
>> Bio::Tools::RestrictionEnzyme has some serious problems with certain
>> custom enzymes).
>
> Did you try the new Bio::Restriction classes?
>
>
> Brian O.
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Tobias
> Sent: Monday, November 03, 2003 9:03 AM
> To: Bioperl
> Subject: [Bioperl-l] bioperl and Bio::Factory::EMBOSS via cgi...
> permissionproblems?
>
> Hi,
>
> I have to run a restriction analysis through EMBOSS restrict (as
> Bio::Tools::RestrictionEnzyme has some serious problems with certain
> custom enzymes). Now everything runs fine when invoked from
> commandline, but when I run the script  through browser and apache I
> get an error:
> Can't call method "run" on an undefined value at ..
> when telling my EMBOSS program to run
>
> seems that I don't get a proper connection to the EMBOSS programs (i
> also can't get version information, nor program descriptions...)
>
> could that be permission problems of the apache user (my EMBOSS
> executables are world read- and executable)?
> someone has similar setup (bioperl and EMBOSS via cgi) and knows where
> to look at?
>
> best regards
> Tobias
>
> Dr. Tobias Straub
> Molecular Biology
> Adolf Butenandt Institut, LMU
> Schillerstr. 44
> 80336 München, Germany
>
> Tel: +49-89-5996439
> Fax: +49-89-5996425
>
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