Problems about Gramene installation

[Steven Schmidt]

Hello Laurent,

I should have release 13 available on the web site tomorrow.
This should answer your questions.
Sorry for the delay.

-Steve

On Monday 15 March 2004 04:35 am, laurent.viau at bayercropscience.com wrote:
> Hello,
>
> I have many questions about the Gramene installation. Indeed, We tried to
> install Gramene since 3 weeks, but we didn't succeed it.
> It exists many inconsistencies in your package.
>
> - First, I would like to know why the release 13 is not available on your
> ftp server (only the release 11 is available !) ?
> So, maybe it explains the different problems we have :
>
> Some majors problems are the wrong SQL requests in your Perl scripts :
> For example, some requests are :
> "SELECT feature.hid,contig.id,feature.seq_start,feature.seq_end,analysis.db
>                                 FROM feature,contig,analysis
>                                 WHERE hid $comparator '$keyword'
>                                 AND feature.contig=contig.internal_id
>                                 AND feature.analysis=analysis.id
>                                 ORDER BY analysis.db,feature.hid"
>
> (in the script unisearch).
>
> However, the table FEATURE doesn't exist in any ORACLE schema available on
> the tfp site ?!
> Therefore, the field "internal_id" int the table "CONTIG" doesn't exist ?!
>
> Many requests such as the request above have been found in the main
> programs of Gramene !!
> Typically, it seems that it exists some inconsistencies between the ORACLE
> schemas and the perl modules/perl scripts from Gramene ?!
>
> - We obtained also a "classic" error when we try to access to the "Marker
> search" or the "Rice Genome Browser".
> "Can't locate object method "request" via package "Apache" at
> /data/private/Gramene_files/cgi-bin/map/marker_view.cgi line 354."
>
> However, our Apache package seems to be well installed (we make the
> verification "print STDERR map { "$_ $INC{$_}\n" } sort keys %INC;" and
> @INC is well "fixed up" in the <Perl> section of httpd.conf). Is there a
> specific perl module "request.pm" to be install in the Apache package or
> another thing to do ??
>
> Thanks a lot for your help !
>
> Best regards,
>
> Laurent
>
> Laurent VIAU
> Bayer CropScience
> mail : laurent.viau at bayercropscience.com

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977
Maybe someday I'll start following my own advice.