[Bioperl-l] FW: blast module errors with web app
Samantha.Thompson at greenbiologics.com
Tue Dec 9 15:42:18 EST 2008
Something interesting did happen.. I think this is probably a Catalyst
issue rather than a BioPerl one.
It still throws the exceptions... but it actually produces a blast
report (so runs the program and the results are produced)...
I will have a go at trying to figure out what the Catalyst stack trace
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Samantha
Sent: 09 December 2008 20:25
To: bioperl-l List
Subject: Re: [Bioperl-l] blast module errors with web app
I tried this env grep, theres nothing in my env variables with regards
With the blast executables I gunzip'd them from ncbi and cp'd the
executables from the blast/bin directory of the distribution to my own
When I run blastall from the command line anywhere it works fine... when
I run it in a normal perl script it works (in that the test script tells
me the number of hits on the command line) .... but when I run it from
within the Catalyst app it throws those exceptions... it may be because
it's trying to create that tmp directory when it runs and isn't able
to... I'm not sure how I would set those in Catalyst, but thats kind of
veering away from BioPerl into Catalyst.. I will try a few more
From: Cook, Malcolm [mailto:MEC at stowers-institute.org]
Sent: 09 December 2008 20:07
To: Samantha Thompson; 'bioperl-l List'
Subject: RE: blast module errors with web app
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?
> -----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
> 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
> ------------- 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
> STACK: Bio::Tools::Run::StandAloneBlast::_runblast
> STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> STACK: Bio::Tools::Run::StandAloneBlast::blastall
> 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...
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
More information about the Bioperl-l