On 6 Jun 2006, at 11:43, Pallavi Sarmah wrote:
Hi
Sorry, Tht was a typographical mistake. I was actually giving the
command
/usr/local/apache/bin/httpd -d biomart-web
ok, in this case it looks like you are running apache without mod_perl
compiled in
try
/usr/local/apache/bin/httpd -l
Compiled-in modules:
http_core.c
mod_env.c
mod_log_config.c
mod_mime.c
mod_negotiation.c
mod_status.c
mod_include.c
mod_autoindex.c
mod_dir.c
mod_cgi.c
mod_asis.c
mod_imap.c
mod_actions.c
mod_userdir.c
mod_alias.c
mod_access.c
mod_auth.c
mod_so.c
mod_setenvif.c
mod_perl.c
and see if you are seeing mod_perl.c
among listed modules
a.
Regards,
Pallavi
-----Original Message-----
From: Arek Kasprzyk [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 06, 2006 3:50 PM
To: Pallavi Sarmah
Cc: [email protected]
Subject: Re: [mart-dev] cannot connect to the server
On 6 Jun 2006, at 10:56, Pallavi Sarmah wrote:
Hi
As I was nt being able to connect to the database, so I shifted all
the
files to my laptop. Here I m being able to import msd_mart_4 bt I m nt
being able to connect to the server.
When I give to command
/usr/local/apache/bin/httpd.conf -d biomart-web
I get the following error msg
Syntax error on line 11 of biomart-web/conf/httpd:
Invalid command '<Perl>', perhaps mis-spelled or defined by a module
not
included in the server configuration.
Hi Pallavi,
you need to double check your command. It should be
/usr/local/apache/bin/httpd -d biomart-web
rather than what you have below:
/usr/local/apache/bin/httpd.conf -d biomart-web
it this still causing you problems let us know,
a.
Now I have FC5, with the same files of biomart-web, it was working
fine
in FC4
Regards,
Pallavi
-----Original Message-----
From: Arek Kasprzyk [mailto:[EMAIL PROTECTED]
Sent: Thursday, June 01, 2006 6:10 PM
To: Pallavi Sarmah
Cc: mart-dev (E-mail)
Subject: Re: [mart-dev] cannot connect to local database.
On 1 Jun 2006, at 05:58, Pallavi Sarmah wrote:
Hi
Hi Pallavi,
I ve sent a mail on 30 th may. Since I have received no reply and
also
it didn't appear in the mail archive I m afraid it must have nt been
delivered. I m forwarding the mail again.
Waiting for a suggestion.
this is because you sent your email directly to me rather than to
mart-dev :-)
It is always safer to send an email to the list because there are more
people
who could respond quickly.
The problem you describe is best tested by writing a simple java class
which connects to the database just to check if this some sort of
JDBC/
db privileges problem or rather a BioMart problem (obviously run from
the
same machine and with the same connection string). Could you check
that and tell us if you are able to do it without BioMart code? We'll
then
look into this in more detail
cheers,
a.
Thank you
Regards,
Pallavi
-----Original Message-----
From: Pallavi Sarmah
Sent: Tuesday, May 30, 2006 12:07 PM
To: 'Arek Kasprzyk'
Subject: RE: [mart-dev] cannot connect to local database.
Hi
I am trying to install biomart locally in my machine. Bt I m nt being
able to connect martj to a database. I ve msd_mart_4 table structures
(without data) locally. I ve modified the defaultmartregistry file
both
in martj n biomart-plib. But still I m nt being able to connect and
the
error msg that I get is as follows
Include a correct meta_version_version__main table
entry:java.sql.SQLException:Invalid authorization specification
message
from server: "Access denied for user
'root'@'localhost.localdomain'(using password:YES)"
While root do have access to the database. I ve tried with other
users
bt still I get the same msg. I am also sending u the
defaultmartregistry
file for yr reference.
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE MartRegistry (View Source for full doctype...)>
- <MartRegistry>
<MartDBLocation name="Local BioMart"
displayName="Local BioMart Database"
databaseType="mysql"
host="localhost"
port="3306"
database="msd_mart_4"
schema="msd_mart_4"
includeDatasets=""
user="root"
password="pallu"
visible="1"
default=""
martUser=""
/>
</MartRegistry>
Regards,
Pallavi
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-
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
-----------------------------------------------------------------------
-
-------
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-
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
-----------------------------------------------------------------------
-
-------
------------------------------------------------------------------------
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
------------------------------------------------------------------------
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