Hi all,
I am trying to configure Biomart on my workstation. But I am unable a
database connection on biomart-web web application, for martj-0.4, I
have managed to obtain a connection but I receive “no datasets in this
database” message when I attempt an import. When I fire up apache web
server and supply the path to biomart-web directory I get the error
below[^].
For both the biomart-web and martj-0.4, I have modified the
“defaultMartRegistry” accordingly to match the database connection
requirements.
I have setup a local msd_mart_4 database with data and schema definition
from “ftp://ftp.ebi.ac.uk/pub/databases/biomart/current/msd_mart_4/” and
populated all the meta_% tables with the exception of meta_interface and
meta_user tables whose sqldump data files appear to be empty, I however
did not populate the msd_% tables.
Regards,
Allan.
[^]
[EMAIL PROTECTED] biomart-web.other]$ date;time
/usr/local/ASF/httpd/apache_1.3.35/bin/httpd -d
/usr/local/src/biomart/biomart-web.other/biomart-web;date;
Fri May 12 12:01:06 SAST 2006
Starting up Ensembl server on host: fusion.sanbi.ac.za:9999
Loading perl startup file...
==============================================================================
[MARTCONF][INFO] Retrieving configuration:
------------------------------------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not connect to database msd_mart_4:
SKIPPING at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not load Registry from database
dbi:mysql:database=msd_mart_4;host=localhost;port=3306, SKIPPING
Syntax error on line 246 of
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:
-------------------- EXCEPTION --------------------
DATE: 12-MAY-2006
MSG: Problems with the retrival of dataset configuration
Please check:
that your mart Registry files contains correct connection params,
that you are using the correct version on XML::Simple,
that BioMart databases contain a populated meta_conf tables and
that you have set martUser correctly if you are running in restricted
data access mode (populated meta_conf__user__dm)
STACK BioMart::Initializer::_new
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Initializer.pm:172
STACK BioMart::RootI::new
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/RootI.pm:54
STACK (eval)
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup:86
STACK (eval)
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:241
STACK toplevel
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup:0
-------------------------------------------
at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup
line 86
Compilation failed in require at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf
line 241.
real 0m2.858s
user 0m0.600s
sys 0m0.148s
Fri May 12 12:01:09 SAST 2006
