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

[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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