<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Todd,<div><br></div><div>Sorry! I should have confirmed that it was still down before replying to Wes. Glad it's back up. It trances for me with the default selection for the SO file, but works if I pick SOFA latest.</div><div><br></div><div>Subsuming into gmod.org or into the SO project (that's where the top Google hit for GFF3 spec is) would make a lot of sense. I downloaded the trunk version from sourceforge and it was pretty easy to get it working on our server:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://ecolihub.net/cgi-bin/validate_gff3_online/validate_gff3_online">http://ecolihub.net/cgi-bin/validate_gff3_online/validate_gff3_online</a></div><div><br></div><div>It looks like the one at Wormbase may still be Payan's. The one from trunk looks like Zheng's. At least it has a different version number. It was pretty easy to set up, but I did have to make one change that may be a Mac Perl dialect thing. In GFF::Online.pm I had to change</div><div><br></div><div><div><div> my $file_length = `wc -l $report_file` =~ /^(\d+)/; </div><div><br></div><div>in sub _store_report_file_info to two lines</div><div><br></div><div><div> my $file_length = `wc -l $report_file`;</div><div> $file_length =~ /^(\d+)/; </div><div><br></div></div></div></div><div>There may be a few other things to tweak. I'm trying to figure out how it decides what the latest SO.obo file is.</div><div><br></div><div>Jim</div><div><br><div><div>On Sep 20, 2009, at 6:11 PM, Todd Harris wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Jim, Wes -<br><br>I've used our very own GFF3 validator on-and-off over the past two<br>years. Although we have had some downtime with the validator due to<br>migrating services to a new hosting facility and new hardware, it is<br>functioning now.<br><br>Still, I think it makes sense for this service to be subsumed by GMOD,<br>with interested users assuming maintenance of the code. The original<br>developer of the validator left WormBase years ago. At that time,<br>there was some discussion of handover to GMOD but that clearly never<br>got very far.<br><br>Zheng Zha has made some changes (principally updating the version of<br>the sequence ontology file; the WormBase validator uses a very old<br>version). This represents the most logical branch of code for import<br>to the GMOD repository.<br><br>I'm happy to check it in and help set up an instance on GMOD.org if I<br>can get shell access to the machine.<br><br>Todd<br><br><br><br><br>On Sun, Sep 20, 2009 at 4:25 PM, Jim Hu <<a href="mailto:jimhu@tamu.edu">jimhu@tamu.edu</a>> wrote:<br><blockquote type="cite">The Wormbase gff validator has been down for a long time. The pathogen<br></blockquote><blockquote type="cite">portal one is not very good. The one that should be at Wormbase should be<br></blockquote><blockquote type="cite">available somewhere in the (formerly cvs) svn repository.<br></blockquote><blockquote type="cite">I should try to put a copy up on one of our public servers.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Jim<br></blockquote><blockquote type="cite">On Sep 14, 2009, at 11:41 PM, Dave Clements, GMOD Help Desk wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi Wes,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks for the heads up on the GFF3 validator at WormBase. I don't<br></blockquote><blockquote type="cite">know what happened to it, but I'll investigate, and drop the link.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">For the validator from pathogenportal, try dropping everything between<br></blockquote><blockquote type="cite">line 2 and the line that says =cut.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Dave C<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Mon, Sep 14, 2009 at 8:47 PM, Wes Barris <<a href="mailto:wes.barris@csiro.au">wes.barris@csiro.au</a>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The GFF3 validation link to wormbase on this page:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://gmod.org/wiki/GFF3#GFF3_Validation">http://gmod.org/wiki/GFF3#GFF3_Validation</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">results in an error. I don't know whether or not wormbase is still<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">providing a gff3 validator.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Also, the gff3 validation perl code from the same page:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://www.pathogenportal.org/resources/gff3Valid.pl">http://www.pathogenportal.org/resources/gff3Valid.pl</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">has errors in it:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">perl -c gff3Valid.pl<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Number found where operator expected at gff3Valid.pl line 8, near "GFF3<br></blockquote><blockquote type="cite">1.01"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> (Do you need to predeclare GFF3?)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Bareword found where operator expected at gff3Valid.pl line 8, near "1.01<br></blockquote><blockquote type="cite">spec"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> (Missing operator before spec?)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Bareword found where operator expected at gff3Valid.pl line 10, near "//www"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> (Missing operator before www?)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Number found where operator expected at gff3Valid.pl line 22, near "over 4"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> (Do you need to predeclare over?)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">syntax error at gff3Valid.pl line 8, near "GFF3 1.01"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Unmatched right curly bracket at gff3Valid.pl line 190, at end of line<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">syntax error at gff3Valid.pl line 190, near "}"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">gff3Valid.pl had compilation errors.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Wes Barris <<a href="mailto:wes.barris@csiro.au">wes.barris@csiro.au</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">------------------------------------------------------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Come build with us! 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