Hi, Thanks for your help Arek, I've been able to solve the problem.
2011/5/3 Arek Kasprzyk <[email protected]> > Hi Amadis, > The user that you are using can be read only but needs to be able to > connect from the host that you are running biomart server on and have access > privileges to the database and tables that you want to query. First try to > rule out all potential 'non-biomart' problems. The simplest test is to try > to query your database from mysql client running on the same host as your > biomart server. If this works writing a simple perl script querying the > same tables and run it from the same host as your biomart server to make > sure that the DBI/DBD install works correctly. > > a > > *Arek Kasprzyk** > *Director, Bioinformatics Operations and Principal Investigator > > *Ontario Institute for Cancer Research* > MaRS Centre, South Tower > 101 College Street, Suite 800 > Toronto, Ontario, Canada M5G 0A3 > > Tel: 416-673-8559 > Toll-free: 1-866-678-6427 > www.oicr.on.ca > > > Administrative Assistant: [email protected] > > > > This message and any attachments may contain confidential and/or privileged > information for the sole use of the intended recipient. Any review or > distribution by anyone other than the person for whom it was originally > intended is strictly prohibited. If you have received this message in error, > please contact the sender and delete all copies. Opinions, conclusions or > other information contained in this message may not be that of the > organization. > > From: Amadis Pages <[email protected]> > Date: Tue, 3 May 2011 06:45:56 -0400 > To: "[email protected]" <[email protected]> > Subject: [BioMart Users] MySQL user privileges > > Hi, > > I've recently installed Biomart in order to make some of my lab's data > publicly available in the future. > > I'm using a *martDBLocation.xml*-style registry file. I've created a MySQL > user with USAGE privileges on the database I'm using to store the data, but > when I try to run the configure.pl script, the following error shows up: > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > COULD NOT CONNECT TO DATABASE xxxxxx.CHECK YOUR SETTINGS > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > What kind of permissions should I grant to the user that appears in the > registry file? I do not feel comfortable giving this user privileges to > modify the database content. Below you can find a copy-paste of the registry > file: > > <MartDBLocation > ... > user = "rgmartuser" > password = "xxxxxxxxxx" > visible = "1" > default = "" > includeDatasets = "" > martUser = "" > /> > > Thanks a lot in advance for your help. Please let me know if this is not > the proper mail to send this kind of inquiries. > > Best regards, > AmadÃs > >
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