Hi Thanks Hans. I was looking but not seeing and had an extra '/' after mysql: that was causing my problems. DataLibraries look exactly like what I need. Now that I've noticed the sitemap I see there's lots of extra documentation I'd been not seeing, which is great. Now to setup an admin user... Thanks for the pointers :) Nathaniel On 11/03/10 14:55, Hotz, Hans-Rudolf wrote:

Nathaniel

Try:

mysql://user:password@localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock (exchanging 'user' and 'password' according to your settings)

or have a look at Nate Coraor's reply to a similar e-mail on this 'galaxy-user' list last Tuesday.

And instead of uploading files have you looked at the possibilities of using 'DataLibraries'? see: http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles

Hans

...

Hi

I have set galaxy to use mysql on localhost but I could not workout the syntax for the database_connection line to specify a username and password. Is this possible? I'm using Ubuntu so as per the install guide I have this

database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock

I wanted to try mysql to see if it was faster for uploads of very large NGS files. At the moment even uploading a file from the localhost is very very slow. Is this normal or are there some ways to speed it up? My fastq files are all> 10GB.

Maybe using Galaxy isn't the right way to go and I should use the tools locally but as NGS handling is in there I am guessing large files were in mind?

Thanks

Nathaniel

-- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street@plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org