Mysql is on an Apache server.
I created a database called 'yeast' by typing the command from my machine (connecting on another server):
Synopsis:
mysql - p -h 'server_name' -P 'port_number' -e 'create database yeast'
(it works).
The next step is to load the database with data.
This is accomplished by loading the database from a tab-delimited file containing the genomic annotations in GFF format.
The Bioperl distribution comes with this Perl script for loading Bio::DB::GFF databases.
But when I try to load the database from my machine with a Perl script: bulk_load_gff.pl - d yeast sample_data/yeast_data.gff
I get :
DBI connect('yeast','',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /local/gensoft/lib/perl5/vendor_perl/5.8.0/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm line 140
------------- EXCEPTION -------------
MSG: Can't connect to database: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
STACK Bio::DB::GFF::Adaptor::dbi::caching_handle::new /local/gensoft/lib/perl5/vendor_perl/5.8.0/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm:90
STACK Bio::DB::GFF::Adaptor::dbi::new /local/gensoft/lib/perl5/vendor_perl/5.8.0/Bio/DB/GFF/Adaptor/dbi.pm:74
STACK Bio::DB::GFF::Adaptor::dbi::mysql::new /local/gensoft/lib/perl5/vendor_perl/5.8.0/Bio/DB/GFF/Adaptor/dbi/mysql.pm:271
STACK Bio::DB::GFF::Adaptor::dbi::mysqlopt::new /local/gensoft/lib/perl5/vendor_perl/5.8.0/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm:149
STACK Bio::DB::GFF::new /local/gensoft/lib/perl5/vendor_perl/5.8.0/Bio/DB/GFF.pm:550
STACK toplevel ../bulk_load_gff.pl:104
--------------------------------------
Is somebody have an idea ??
Thanks a lot,
Hafed
