On 23 Jan 2007, at 15:49, Camargo R D S wrote:
Hi Arek,
no problem but I am a bit confused here. Can you actually
connect to your database using mysql client?
ei can you do
mysql -uroot -hlocalhost ensembl_mart_42
and see mart tables? if you can the software will also be able to
The error below suggests that you have at least 'meta' table missing
from there. Can you try the command above and on mysql prompt
say
'show tables'
and tell me what you are seeing?
Done that before too, but I can not see the tables
[EMAIL PROTECTED]:/home/renata/BioMart/biomart-perl# mysql -u root -h
localhost
ensembl_mart_42 -p
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 9 to server version: 5.0.24a-Debian_9-log
Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
mysql>
mysql> show tables
-> ;
Empty set (0.01 sec)
mysql>
ok, I understand now. Renata - this is a problem with mysql
data upload not BioMart. You need to make sure
that you perform 'mysqlimport' on your 'txt' table. Please
consult online mysql manual
a.
What are the extensions for the tables in ensembl_mart_42?
I have got:
dm.txt.table
main.txt.table
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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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