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

[Tim Booth]

Hi Simon,

Please do not try to fix the database by following manual setup
instructions in the upstream documentation.  The entire point of this
packaging exercise was to avoid manual and potentially insecure
configuration of MySQL!

I got a long reply from the Stacks author regarding my approach to the
packaging.  He pointed out that my default assumption of naming the
database after the user was wrong - the database should always be named
after the experiment - which I can easily do (and you can do so now
using the -d flag in any case).  Apart from that he pointed out a couple
of minor issues I will go ahead and change but the database security
settings will stay as they are in the current package.

The actual error you have relates to the debian-sys-maint account which
is a standard part of the Debian MySQL installation and allows the Deb
system scripts to configure the database.  If this account isn't logging
in then there is a problem with your MySQL installation.  Please try
reinitialising it like so:

$ sudo mv /etc/mysql/debian.cnf /etc/mysql/debian.cnf.bak
$ sudo dpkg-reconfigure -plow mysql-server-5.5

Does that help?

Cheers,

TIM

On Sun, 2015-02-08 at 10:11 +0000, Steve Moss wrote:
> 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
> Steve Moss on about.me
>  

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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