Thanks for fielding that one, Dave. I have been out of email contact for a few days.<br><br>Sheldon<br><br>
<br><br><div class="gmail_quote">On Fri, Mar 5, 2010 at 3:33 PM, Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:help@gmod.org">help@gmod.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Hi Christoph,<br></div><div><br></div><div>Are you using GBrowse 2? PrimerDesigner does not yet work with 2. See <a href="http://article.gmane.org/gmane.science.biology.gmod.gbrowse/4292" target="_blank">http://article.gmane.org/gmane.science.biology.gmod.gbrowse/4292</a>.</div>
<div><br></div><div>Dave C</div><br><div class="gmail_quote"><div><div></div><div class="h5">On Thu, Mar 4, 2010 at 8:23 AM, Christoph Grunau <span dir="ltr"><<a href="mailto:christoph.grunau@univ-perp.fr" target="_blank">christoph.grunau@univ-perp.fr</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><div style="word-wrap: break-word;"><div>Dear <span style="font-family: monospace; white-space: pre;">Jim Kent,</span></div>
<div><font face="monospace"><span style="white-space: pre;"><br></span></font></div><div><font face="monospace"><span style="white-space: pre;">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 <span style="font-family: Helvetica; white-space: normal;">Generic genome browser version 1.7. I followed the procedure on <a href="http://gmod.org/wiki/PrimerDesigner.pm" target="_blank">http://gmod.org/wiki/PrimerDesigner.pm</a></span></span></font></div>
<div><br></div><div>I downloaded and installed primer3. Standalone version works and is located in /usr/local/bin.</div><div><br></div><div>Bio::PrimerDesigner I installed via CPAN:</div><div><br></div><div><div>perl -MCPAN -e 'install Bio::PrimerDesigner'</div>
<div><br></div></div><div>No error messages.</div><div><br></div><div>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."</div>
<div><br></div><div>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 <a href="http://cbetmcalcul.univ-perp.fr" target="_blank">cbetmcalcul.univ-perp.fr</a> Port 80</div>
<div><br></div><div>When I comment like this:</div><div><div>plugins = BatchDumper FastaDumper RestrictionAnnotator FilterTest Aligner OligoFinder Submitter GFFdumper #PrimerDesigner</div><div><br></div></div><div>GBrowse works again.</div>
<div><br></div><div>The error_log says:</div><div><br></div>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.<div>
<br></div><div><div>The Perl version is:</div><div>perl, v5.8.8 built for x86_64-linux-thread-multi</div><div><br></div><div>----------------------------------------------------</div><div>Modules are located in:</div><div>
<div><div>ls /usr/lib/perl5/site_perl/5.8.8/Bio/PrimerDesigner -la</div><div>total 76</div><div>drwxr-xr-x 2 root root 4096 mar 4 12:16 .</div><div>drwxr-xr-x 49 root root 4096 mar 4 12:16 ..</div><div>-r--r--r-- 1 root root 1028 mar 4 12:16 Config.pm</div>
<div>-r--r--r-- 1 root root 8724 mar 4 12:16 <a href="http://epcr.pm" target="_blank">epcr.pm</a></div><div>-r--r--r-- 1 root root 8808 mar 4 12:16 <a href="http://ispcr.pm" target="_blank">ispcr.pm</a></div><div>-r--r--r-- 1 root root 18626 mar 4 12:16 <a href="http://primer3.pm" target="_blank">primer3.pm</a></div>
<div>-r--r--r-- 1 root root 3595 mar 4 12:16 Remote.pm</div><div>-r--r--r-- 1 root root 6284 mar 4 12:16 Result.pm</div><div>-r--r--r-- 1 root root 7986 mar 4 12:16 Tables.pm</div><div><br></div><div>----------------------------------------------------------</div>
<div><br></div><div>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.</div><div><br></div><div><a href="http://cbetmcalcul.univ-perp.fr/cgi-bin/primer_designer.cgi" target="_blank">http://cbetmcalcul.univ-perp.fr/cgi-bin/primer_designer.cgi</a></div>
<div><br></div><div>Output:</div><div>Software error: No config info provided at /xxx/xxx/cgi-bin/primer_designer.cgi line 48.</div><div><br></div><div><br></div><div>Thanks a million for any idea how to solve the problem.</div>
<div><br></div><div>Very best regards - Christoph Grunau</div></div></div></div><br><br><div> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div>
--</div><div>Christoph Grunau</div><div>Maître de Conférence/Associate Professor</div><div>UMR 5244 CNRS-EPHE-UPVD</div><div>Biologie et Ecologie tropicale et méditerranéenne</div><div>CBETM, Université de Perpignan</div>
<div>52 Avenue Paul Alduy</div><div>66860 Perpignan Cedex, France</div><div>Tel 33 (0)4.68.66.21.80</div><div style="margin: 0px;">Fax 33 (0)4.68.66.22.81</div><div style="margin: 0px;">
<a href="http://cbetm.univ-perp.fr" target="_blank">http://cbetm.univ-perp.fr</a>/</div><div style="margin: 0px;"><br></div><br></span></span></span></span><br></span> </div>
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