[Bio-Linux] Stacks RAD-seq software on Bio-Linux

[Steve Moss]

Dear Simon,

It seems as though it can't authenticate with your database. See this link
http://creskolab.uoregon.edu/stacks/manual/#install specifically "Section
2.3 Edit the MySQL configuration file" that details setting up MySQL users.
Use mysql -u root to login to the MySQL shell and add new users. You should
then edit /usr/local/share/stacks/sql/mysql.cnf to include the appropriate
user and password for connection. It's not a good idea to use root for
stacks to connect, so you should create an additional stacks user in MySQL.

Cheers,

Steve

Message: 1
> Date: Fri, 6 Feb 2015 19:38:56 +0000
> From: Simon Wagstaff <Simon.Wagstaff at lstmed.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] Stacks RAD-seq software on Bio-Linux
> Message-ID: <3ED46ED7-9B83-43C0-8C7A-1D2D5D578329 at lstmed.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Tim,
> Thanks again for doing this. I?ve installed stacks web but got some errors
> (below) when attempting to create the database. I?m not familiar with how
> it works so not sure if this is a problem?
>
> Thanks,
>
> Simon
>
>
> simonw at PowerEdge-R820[simonw] sudo stacks-setup-database gweedall     [
> 7:26PM]
> ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost'
> (using password: YES)
> Making database gweedall_radtags for gweedall
> ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost'
> (using password: YES)
> Aborting.
> simonw at PowerEdge-R820[simonw]                                         [
> 7:27PM]
>
>
> _________________________________
>
> Simon Wagstaff
> Tel: +44-(0)151-705-3164
> Fax: +44-(0)151-705-3371
> email: simon.wagstaff at lstmed.ac.uk<mailto:simon.wagstaff at lstmed.ac.uk>
>



-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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