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

[Rob Edwards]

Tobias,

You could try the newer Bio::Restriction modules available in bioperl 
1.3. It should be able to handle custom enzymes a lot better.

Rob


On Monday, November 3, 2003, at 08:02  AM, Tobias wrote:

> 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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