Hi Dave and all,<br> I have actually (semi-)resolved the issue. First I should have noted that I added an extra line of code so when I get the error on line 440, that actually refers to line 439 of UcscConservation.pm.<br>
<br>It seems the issue is that the trackDB table in the database I was using did not have entries for all the conservation tracks. I simple switched to an alignment that had the proper entry in the trackDB table. <br><br>
-Bill<br><br><div class="gmail_quote">On Thu, May 14, 2009 at 4:41 PM, Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</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;">
Hi Bill,<br>
<br>
The error you are seeing is actually a warning, and is often ignorable<br>
in Perl programs. However, I don't think that is the case here. Line<br>
440 of the latest UcscConservation.pm is:<br>
<br>
412 sub annotate {<br>
413 my $self = shift;<br>
414 my $segment = shift;<br>
415 my $config = $self->configuration;<br>
416 $self->get_browser_config_settings() unless $self->{db};<br>
417 return unless defined %$config;<br>
418<br>
419 warn("UcscConservation annotate start " . `date`) if DEBUG;<br>
420<br>
421 my $ref = $segment->seq_id;<br>
422 my $abs_start = $segment->start;<br>
423 my $abs_end = $segment->end;<br>
424<br>
425 my $feature_list = $self->new_feature_list;<br>
426<br>
427 my @wigMafTracks = grep {($config->{$_} && s/^enable_// &&<br>
428 $self->table_exists($_, $ref))}<br>
keys %$config;<br>
429 if (scalar(@wigMafTracks) == 0) {<br>
430 if ($self->{default_enable}) {<br>
431 @wigMafTracks = grep {s/^enable_// &&<br>
$self->table_exists($_, $ref)}<br>
432 keys %{$self->{default_enable}};<br>
433 } elsif ($config->{'enableAll'}) {<br>
434 @wigMafTracks = $self->list_tracks_by_type('wigMaf');<br>
435 }<br>
436 }<br>
437 @wigMafTracks = $self->sort_by_trackDb_priority(@wigMafTracks);<br>
438 foreach my $track (@wigMafTracks) {<br>
439 my $label = $self->get_trackDb_val($track, 'longLabel') . ' (UCSC)';<br>
440 $feature_list->add_type($track=>{glyph => 'ucsc_glyph',<br>
441 key => $label,<br>
442 });<br>
443 my $feature = $self->wigMaf_feature($track, $ref,<br>
$abs_start, $abs_end);<br>
444 $feature_list->add_feature($feature, $track);<br>
445 }<br>
446 warn("UcscConservation annotate end " . `date`) if DEBUG;<br>
447 return $feature_list;<br>
448 }<br>
<br>
According to my limited Perl understanding, I think all variables in<br>
line 440 should be defined, so I have no idea what is going on here.<br>
<br>
Does anyone else have any insight into what Bill is seeing? Could<br>
this error even be causing what he is seeing?<br>
<br>
Thanks,<br>
<br>
Dave C.<br>
<div><div></div><div class="h5"><br>
On Tue, May 12, 2009 at 9:17 AM, Bill Pulec <<a href="mailto:wpulec@gmail.com">wpulec@gmail.com</a>> wrote:<br>
> Hi All,-<br>
> I have some conservation tracks that I have been trying to add to a<br>
> database using the UCSC plug-in, but I always get an error when I try to<br>
> open the tracks in Gbrowse. I know that the UCSC plug-in,<br>
> UcscTrackImage.conf and the hgcentral database must be working because I<br>
> have set up conservation tracks for other databases, and they work fine.<br>
> When grbrowse loads the failing conservation tracks all the tracks and the<br>
> settings below the tracks do not load.<br>
><br>
> There is an error in the error log:<br>
><br>
> Use of uninitialized value in concatenation (.) or string at<br>
> /etc/httpd/conf/gbrowse.conf/plugins/UcscConservation.pm line 440., referer:<br>
> <NameOfMyServer><br>
><br>
> This seems to me like UcscConservation.pm can't find the correct file on my<br>
> hard drive that the MySQL tables refer to, but the file seems to be in the<br>
> correct location with the correct file name. So I am not sure why it cannot<br>
> find the file.<br>
><br>
> If anyone has any insights into what is going on it would be greatly<br>
> appreciated.<br>
><br>
> Thanks,<br>
> Bill<br>
><br>
><br>
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