Re: gbrowse 2 and renderfarm

Hi Scott, Lincoln,

when I checked the slave error logs. I see
Can't locate Bio/DB/Das/Chado.pm

So I add in /etc/default/gbrowse_slave the path of Bio::DB::Das::Chado and now it's work

Thanks,

Baptiste

Scott Cain wrote:

Ah, OK.  Baptiste let me know if you find anything out.  I did set up a simple system (no renderfarm so far) and found that as you wrote, it works fine (although very much faster than without.  That was incredibly easy to set up--Thanks, Lincoln).

Scott


On Sep 2, 2009, at 2:14 PM, Lincoln Stein wrote:

Hi Baptiste, Scott,

This message happens when the object is corrupted for any reason. Is the error occurring on the slave or the master? My guess is that the slave is missing some library needed for the Chado connection and is throwing an error and returning a partial object to the master. Check the slave error logs.

Lincoln

On Wed, Sep 2, 2009 at 1:11 PM, Scott Cain <scott@...> wrote:
Hi Baptiste,

That is really interesting, and I have no idea what might be going
on.  If anybody else has any suggestions, I'd like to hear about them.

In the meantime, I'll set up a system with modperl to see if I can
reproduce it.

Scott


On Sep 2, 2009, at 12:09 PM, Baptiste Brault wrote:

> Hi all,
>
> I tried gbrowse2 with mod perl + renderfarm. Everything is okay for
> GFF,
> Mysql, Bio::SeqFeature::Store.
>
> I also try with Postgresql/ Chado. I get this error message :
>
> Magic number checking on storable string failed at ../../lib/
> Storable.pm
> (autosplit into ../../lib/auto/Storable/thaw.al) line 363, at
> /home/projects/gpi/ggb/Generic-Genome-Browser-2.00-beta/lib/perl5/
> sun4-solaris-thread-multi-64/Bio/Graphics/Browser/RenderPanels.pm
> line 653, referer:
> http://localhost:1671/gb2/gbrowse/Botrytis/?name=bt4ctg_0111%3A3858..6529
>
> So, tracks aren't displayed.
> My configuration works without mod perl + renderfarm, mod perl only.
>
> Could you please help me ?
>
>
> Thanks,
>
> Baptiste
>
> --
> Baptiste Brault
> INRA URGI/BIOGER, Bat 18
> Route de Saint Cyr 78026 Versailles
> baptiste.brault@...
> tel:+33 1 30 83 37 70
>
>
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research





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trial. Simplify your report design, integration and deployment - and focus on
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--

Baptiste Brault
INRA URGI/BIOGER, Bat 18
Route de Saint Cyr 78026 Versailles baptiste.brault@...
tel:+33 1 30 83 37 70