Interest in Gramene

Wed Apr 14 18:16:50 EDT 2004

Hi Laurent,

0. As you probably noticed, gramene.org doesn't accept .doc and 
Lincoln 
doesn't accept .zip.  This is because they can carry viruses. It's 
best to 
send us plain text, or, if the formatting is important, rtf or html.

1. I've fixed some obsolete things in gramene_installation.html 
bioperl version should be 1.+, not 0.7
Use gramene_ensembl/conf, not gramene_ensembl/conf.ensembl

1a.  This document needs some more changes relating to the 
configuration.
We use two web servers - the EnsEMBL, protein, ontology, and phenotype 
pages 
are proxied to a backend server.  CMap & qtl modules can be on either.
The front-end config is in gramene/conf, the backend in 
gramene_ensembl/conf.
You probably want to use one server.  The installation instructions 
say to use 
the gramene_ensembl configuration and edit it in certain ways.  But 
probably 
there are more edits not contained in these instructions.  Maybe Alex 
Li can 
provide information on what he did.  I will look into merging the 
configs and 
using parameters to make it work with one or two servers.
Note that EnsEMBL does not play well with other sites on the same 
server.  
Also, the server startup takes a while because it checks the database 
for 
each species to see what features exist.  If you restart apache while 
the 
database is down or inacessible then EnsEMBL will not work.

2.  ACTION :
Click on "Genome Browser" link 
(www.bayer-gramene.org/japonica/mapview?chr=1)                                                                     
Error :
"File does not exist: 
/data/private/Gramene_files/htdocs/japonica/mapview"

This looks like a web server configuration problem.
initHandler in gramene_ensembl/modules/Apache/EnsEMBL/Handlers.pm 
should 
direct /japonica/mapview  to  /perl/default/mapview
with the environment variable ENSEMBL_SPECIES set to japonica, 
assuming 
japonica is one of the values or keys in $ENSEMBL_SPECIES_ALIASES in 
SIteDefs.pm
This line in gramene_ensembl/conf/httpd.conf does it:
@PerlPostReadRequestHandler     = 
('Apache::EnsEMBL::Handlers::initHandler');

3. ACTION :
Click on "Marker" link (www.bayer-gramene.org/db/markers/marker_view) 
:
Error :
"File does not  exist: 
/data/private/Gramene_files/htdocs/db/markers/marker_view"
...
"[Wed Apr 14 09:53:16 2004] [error] (2)No such file or directory: exec 
of 
/data/private/Gramene_files/cgi-bin/markers/marker_view failed

I think this is because /cgi-bin should be Apache::Registry or 
Apache::PerlRun, not really a cgi-bin.  I added this to the install 
docs

4. ACTION :
Click on a chromosome link (www.bayer-gramene.org/perl/mapview?chr=1) 
:
Error :
"[Tue Apr 13 16:54:10 2004] [error] Global symbol 
"$ENSEMBL_CONFIG_FILENAME" 
requires explicit package name at 
/data/private/Gramene_files/lib/modules/SpeciesDefs.pm line 47.
etc.

Thise variables are declared in SiteDefs.pm which Species.pm uses.
And httpd.conf already does a require of SiteDefs.pm and puts the conf 
directory into @INC.
Assuming that httpd.conf is ok, maybe you should put
BEGIN { print STDERR $INC{'SiteDefs.pm'},"\n" } into Species.pm to see 
if 
something has gone astray.

5. Error :
"[Tue Apr 13 17:05:54 2004] [error] Storable binary image v17.33 more 
recent 
than I am (v2.6) at blib/lib/Storable.pm (autosplit into 
blib/lib/auto/Storable/thaw.al) line 363, <FH> chunk 1, at 
/data/private/Gramene_files/lib/modules/SpeciesDefs.pm line 74
Compilation failed in require at 
/data/private/Gramene_files/cgi-bin/mapview 
line 25, <FH> line 1.
BEGIN failed--compilation aborted at 
/data/private/Gramene_files/cgi-bin/mapview line 25, <FH> line 1."

Remove conf/config.packed and restart the server.
Do you have two versions of Storable on your system?

6. ACTION :
Quick Search (with the number ap004078)                                                                 
Error :
"[Tue Apr 13 17:20:00 2004] browser: Can't locate object method 
"request" via 
package "Apache" at 
/data/private/Gramene_files/cgi-bin/searches/browser line 
54."

You have 
use Apache;
in perl.startup, right?
Assuming this script is invoked by Apache::Registry or 
Apache::PerlRun, this 
should not happen.  So fixing the config in that way should fix this 
problem.

-Steve

On Wednesday 14 April 2004 04:30 am, laurent.viau at bayercropscience.com 
wrote:
> Dear Steve,
>
> As you mentioned in your last mail to my collaborator Evelyne James, 
I send
> you the details of the problems we encountered during the 
installation of
> Gramene. You will find attached a Word document containing the 
problems
> which occurs in the Gramene interface and what are the associated 
error
> messages.
>
> (See attached file: Errors.doc.zip)
>
>
> Thank you again for your help.
> Best regards,
>
> Laurent

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