Re: error to reinstall GBrowse v2

Hi,

Your experiment shows that Apache cannot find some required
modules at run time on your server. It's also possible that
your

  /usr/lib/apache2/modules/mod_perl.so

doesn't work with other modules because of the version
mismatch. Please make sure that the mod_perl is right for
perl 5.10.0 and the Apache server. Because mod_perl must be
for a specific Perl *and* Apache version.

I've just successfully installed GBrowse 1.994, and it runs
with mod_perl

  https://slave.molbiol.ox.ac.uk/mgb2/gbrowse/yeast/

or without mod_perl
  https://slave.molbiol.ox.ac.uk/cgi-bin/gbrowse/yeast/

We use httpd-2.2.9-1.fc8 perl-5.8.8-41.fc8 and
mod_perl-2.0.3-14, all from Fedora Core 8 distribution.

After installing all the required packages, we've configured
GBrowse as follows

perl Build.PL --apachemodules=/usr/lib64/httpd/modules \
              --cgibin=/wwwdata/gbrowse-2.0a/cgi-bin \
              --conf=/wwwdata/gbrowse-2.0a/conf \
              --htdocs=/wwwdata/gbrowse-2.0a/htdocs \
              --databases=/wwwdata/gbrowse-2.0a/databases \
              --tmp=/tmp/gbrowse2 \
              --portdemo=8080 \
              --wwwuser=nobody

And below are some relevant entries in Apache configuration
gbrowse2.conf:

ScriptAlias  "/cgi-bin"   "/wwwdata/gbrowse-2.0a/cgi-bin/gb2"
ScriptAlias  "/mgb2"      "/wwwdata/gbrowse-2.0a/cgi-bin/gb2"

<IfModule mod_perl.c>
   PerlModule ModPerl::Registry

   <Location /mgb2>
     SetHandler perl-script
     PerlResponseHandler ModPerl::Registry
     PerlOptions +ParseHeaders
   </Location>
</IfModule>

Hope this encourages you to examine your site installation
and configuration closely to solve the problem. Sorry I cannot
answer other questions you've raised.

Regards,

Zong-Pei


On Mon, 8 Jun 2009, Alessandra wrote:
Date: Mon, 8 Jun 2009 14:37:01 +0200
From: Alessandra <alessandra.bilardi@...>
To: zph@...
Cc: GMOD GBrowse List <gmod-gbrowse@...>
Subject: Re: [Gmod-gbrowse] error to reinstall GBrowse v2

I commented line
LoadModule perl_module /usr/lib/apache2/modules/mod_perl.so

in /etc/apache2/mods-available/perl.load

and I obtain only normal error about page not found when I request
http://gbrowse.cribi.unipd.it/mpublic/gbrowse/vitis_vinifera_8x/

other apache errors log about fpublic are egual.

I have got two directory about perl:

/usr/local/lib/perl/5.10.0/
and /usr/local/share/perl/5.10.0/
but I checked these directories and there are not file in each
directories: there are not file double.

>-------------------------------------------<
others apache error log
>-------------------------------------------<

I'm testing gbrowse mysql databases that they works with gbrowse v1.69
(db_adaptor=Bio::DB::GFF), as
http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/

and if I click one track for gbrowse_details page, I obtain page with
this warning:
"Requested feature not found in database."

instead, when I test others databases with
db_adaptor=Bio::DB::SeqFeature::Store (there are private, with pw, but
if it is important I could create example gbrowse for you) this I
obtain apache error log:

"my" variable $name masks earlier declaration in same scope at (eval
107) line 3.
"my" variable $name masks earlier declaration in same scope at (eval
112) line 3.

Alessandra.

[snip]

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