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

[Simon Wagstaff]

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>




On 23 Jan 2015, at 14:39, Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>> wrote:

Hi All,

A very long time ago, someone asked me if I could put Stacks
(http://creskolab.uoregon.edu/stacks/) on Bio-Linux.  More recently,
other people have asked more insistently if I can do a package, and I
finally have.

So you can "apt-get install stacks" then type:

$ stacks help

To see available commands.

There are various problems with getting Stacks to work well as a
package, especially the database and web viewer bit, which I've split
into a package called "stacks-web".  The standard installation is both
really complex and assumes that you are the sole user on the system, or
at least that you don't care about other users accessing all your stuff.
I think I've made things much neater and simpler, but the upshot is that
most of the regular set-up instructions are misleading for anyone using
this new package.  Essentially there is now just one thing to do -
running:

$ sudo stacks-setup-database <username>

Before that particular user tries to load anything to the database.

If you are interested in using Stacks please let me know if you try
these packages, and let me know if they actually work or if you have any
problems/questions.

Cheers,

TIM

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

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://environmentalomics.org/bio-linux
+44 1491 69 2297

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