[Gmod-help] Problem with GMOD Gbrowse

[Lincoln Stein]

I have not seen this problem before, but if I can reproduce it locally it
should be easy to fix. Can I ask whether the basic display of features is
broken as well, or is it just the error messages and the inability to access
sequence that is problematic?

Lincoln

On Tue, May 11, 2010 at 3:33 AM, Aurélien BERNARD <
arbernard at clermont.inra.fr> wrote:

>  Hello GMOD support team,
>
> First of all I will present myself:
>
> My name is Aurélien Bernard, I'm a software engineer in a french laboratory
> called INRA (National Institute for Agricultural Research)
> I currently work in the development team of a wheat annotation pipeline
> that generate GFF files (TriAnnot pipeline:
> http://urgi.versailles.inra.fr/projects/TriAnnot/index.php).
>
> We have decided to use Gbrowse (1.70) to allow our users to visualize their
> results.
> Please note that Gbrowse is installed on a server of the INRA bioinformatic
> platform (URGI) and used by several INRA laboratories.
> Therefore we can't decide which version to use or when to update Gbrowse.
>
> Since the beginning of my work with Gbrowse I have created a custom
> configuration file, written some Perl functions to exploit popup balloons
> (on hover and on click) and developed a simple plugin for our proper use.
> On URGI's advice we have chosen the following adaptor:
>
> db_adaptor = Bio::DB::SeqFeature::Store
>
> However, when they used a MySQL database we have decided to load GFF files
> into memory:
>
> db_args = -adaptor memory
> -dir '/home/projects/triannot/GFF/'
>
> This choice can be explained by the fact that our pipeline stores GFF
> result files into a particular directory where our users can download them
> (or Gbrowse can read them) for a short period of time (Old files are
> automatically deleted after one or two weeks).
>
> Everything goes well on the different GFF files I have tested separately.
> But, if I try to put several GFF files (each of these files contains a
> sequence in fasta format in its bottom part) in the same directory then
> everything goes wrong:
>
> - My apache error file becomes full of error messages
> - It becomes impossible to access to the sequence of each supernumerary GFF
> file
>
> Example of error message:
>
> [Mon May 03 17:02:43 2010] [error] [client 127.0.0.1] print() on closed
> filehandle GEN3 at
> [Mon May 03 17:02:43 2010] [error] [client 127.0.0.1]
> \t/usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/memory.pmline 598, <GEN5> line 888 (#1)
>
> This problems seems to be directly related to our choice of db_args so I
> give a look to the correspondant BioPerl module (memory.pm).
>
> Line 598 is included in a function with a strange comment line:
>
> # this is ugly
> sub _insert_sequence {
>     my $self = shift;
>     my ($seqid,$seq,$offset) = @_;
>     my $dna_fh = $self->private_fasta_file or return;
>     if ($offset == 0) { # start of the sequence
>        print $dna_fh ">$seqid\n";
>     }
>     print $dna_fh $seq,"\n";
> }
>
> Does a Gbrowse user already encounter this problem ?
>
> Do you have a solution to make it work better ?
>
>
> I thank you in advance for your help !!
>
> Best regards,
>
> Aurélien
>
> --
> Aurélien Bernard
>
> Software engineer
>
> INRA (Institut National de la Recherche Agronomique)
> UMR INRA-UBP 1095
> Génétique, Diversité et Ecophysiologie des Céréales
> 234, Avenue du Brézet
> 63100 Clermont-Ferrand
> FRANCE
>
> Tel: +33 (0)4.73.62.43.37
>
>


-- 
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 at oicr.on.ca>
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