[Gmod-help] Re: [Gmod-gbrowse] PrimerDesigner plugin

[Sheldon McKay]

Thanks for fielding that one, Dave.  I have been out of email contact for a
few days.

Sheldon



On Fri, Mar 5, 2010 at 3:33 PM, Dave Clements, GMOD Help Desk <help at gmod.org
> wrote:

> Hi Christoph,
>
> Are you using GBrowse 2?  PrimerDesigner does not yet work with 2.  See
> http://article.gmane.org/gmane.science.biology.gmod.gbrowse/4292.
>
> Dave C
>
> On Thu, Mar 4, 2010 at 8:23 AM, Christoph Grunau <
> christoph.grunau at univ-perp.fr> wrote:
>
>> Dear Jim Kent,
>>
>> thank you very much for making Primer_Designer available. It looks like a
>> great tool! We would like to use it on our local GBrowse but I have
>> difficulties getting it up and running. We use Generic genome browser
>> version 1.7. I followed the procedure on
>> http://gmod.org/wiki/PrimerDesigner.pm
>>
>> I downloaded and installed primer3. Standalone version works and is
>> located in /usr/local/bin.
>>
>> Bio::PrimerDesigner I installed via CPAN:
>>
>> perl -MCPAN -e 'install Bio::PrimerDesigner'
>>
>> No error messages.
>>
>> When I add PrimerDesigner to the plugin list of GBrowse, the apache web
>> server says "The server encountered an internal error or misconfiguration
>> and was unable to complete your request."
>>
>> Apache/2.2.6 (Fedora) DAV/2 PHP/5.2.4 mod_python/3.3.1 Python/2.5.1
>> mod_ssl/2.2.6 OpenSSL/0.9.8b mod_perl/2.0.3 Perl/v5.8.8 Server at
>> cbetmcalcul.univ-perp.fr Port 80
>>
>> When I comment like this:
>> plugins = BatchDumper FastaDumper RestrictionAnnotator FilterTest Aligner
>> OligoFinder Submitter GFFdumper #PrimerDesigner
>>
>> GBrowse works again.
>>
>> The error_log says:
>>
>> Can't locate object method "new" via package
>> "Bio::Graphics::Browser::Plugin::PrimerDesigner" (perhaps you forgot to load
>> "Bio::Graphics::Browser::Plugin::PrimerDesigner"?) at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/PluginSet.pm
>> line 30.
>>
>> The Perl version is:
>> perl, v5.8.8 built for x86_64-linux-thread-multi
>>
>> ----------------------------------------------------
>> Modules are located in:
>> ls /usr/lib/perl5/site_perl/5.8.8/Bio/PrimerDesigner -la
>> total 76
>> drwxr-xr-x  2 root root  4096 mar  4 12:16 .
>> drwxr-xr-x 49 root root  4096 mar  4 12:16 ..
>> -r--r--r--  1 root root  1028 mar  4 12:16 Config.pm
>> -r--r--r--  1 root root  8724 mar  4 12:16 epcr.pm
>> -r--r--r--  1 root root  8808 mar  4 12:16 ispcr.pm
>> -r--r--r--  1 root root 18626 mar  4 12:16 primer3.pm
>> -r--r--r--  1 root root  3595 mar  4 12:16 Remote.pm
>> -r--r--r--  1 root root  6284 mar  4 12:16 Result.pm
>> -r--r--r--  1 root root  7986 mar  4 12:16 Tables.pm
>>
>> ----------------------------------------------------------
>>
>> I tried to test primer_designer.cgi but can't get it to provide an output.
>> I don't find how to provide the parameters.
>>
>> http://cbetmcalcul.univ-perp.fr/cgi-bin/primer_designer.cgi
>>
>> Output:
>> Software error: No config info provided at
>> /xxx/xxx/cgi-bin/primer_designer.cgi line 48.
>>
>>
>> Thanks a million for any idea how to solve the problem.
>>
>> Very best regards - Christoph Grunau
>>
>>
>>  --
>> Christoph Grunau
>> Maître de Conférence/Associate Professor
>> UMR 5244 CNRS-EPHE-UPVD
>> Biologie et Ecologie tropicale et méditerranéenne
>> CBETM, Université de Perpignan
>> 52 Avenue Paul Alduy
>> 66860 Perpignan Cedex, France
>> Tel 33 (0)4.68.66.21.80
>> Fax 33 (0)4.68.66.22.81
>> http://cbetm.univ-perp.fr/
>>
>>
>>
>>
>>
>> --
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>> CRI UPVD http://www.univ-perp.fr
>>
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>>
>
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