[Bioperl-l] blast module errors with web app

[Cook, Malcolm]

perhaps your environment underl Catalyst server is incomplete....

do this interactively:

> env | grep -i blast


do you see any blast related environment variables?

are they set in the Catalyst server process?

Just thinkin...

Malcolm Cook

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> Samantha Thompson
> Sent: Tuesday, December 09, 2008 1:35 PM
> To: bioperl-l List
> Subject: [Bioperl-l] blast module errors with web app
>
> Hi,
>
>
>
> I seem to be able to get stand alone blast to run ok, using a
> script like the one in the Beginner's HowTo ...
>
> But when running it embedded in my web app I get the following
> errors/exceptions:
>
>
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
>
> MSG: blastall call crashed: -1 /usr/bin/blastall -d  "/src/GBLCCDB16s"
> -i  /tmp/FxXS98W1H0  -o  /tmp/6gp_EnCnsu  -p  blastn
>
>
>
> STACK: Error::throw
>
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:359
>
> STACK: Bio::Tools::Run::StandAloneBlast::_runblast
> /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:813
>
> STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:760
>
> STACK: Bio::Tools::Run::StandAloneBlast::blastall
> /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:570
>
>
>
> This comes from the stack trace of my Catalyst web app....
>
> I wonder if these particular exceptions mean anything to
> anyone. Does BLAST not like the database have folder names in
> it? Maybe theres a problem with the tmp folder not existing
> as part of my web app. Maybe I need to explicitly define the
> -i and -o parameters...
>
>
>
> Thanks,
>
>
>
> Sam
>
>
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