[ensembl-dev] Local MySQL install...
S.P.Moss at 2007.hull.ac.uk
Mon Feb 28 10:18:00 GMT 2011
Excellent thank you! I've updated my script accordingly and added it to my
github here https://github.com/gawbul/bio-misc/blob/master/get_ensembl.pl!
Any input on improvements should be greatly appreciated.
On 23 February 2011 12:00, <dev-request at ensembl.org> wrote:
> Message: 5
> Date: Wed, 23 Feb 2011 11:17:52 +0100
> From: Remo Sanges <noncoding at gmail.com>
> Subject: Re: [ensembl-dev] Local MySQL install...
> To: Steve Moss <S.P.Moss at 2007.hull.ac.uk>
> Cc: dev at ensembl.org
> Message-ID: <4D64DED0.3050201 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Dear Steve,
> in order to use all the functionalities of the compara API you need access
> to an ensembl_compara_XX database as well as to all the core databases of
> the species you are working on.
> Maybe a bit OT but it would be great if you could share your script....
> On 02/18/2011 09:59 AM, Steve Moss wrote:
> > Dear all,
> > I have created a Perl script that automatically retrieves all the
> databases (currently just for core) from the
> ftp.ensembl.org/pub/current_mysql <
> http://ftp.ensembl.org/pub/current_mysql> site directory, extracts them
> and inserts them into a local MySQL database. I am doing lots of parallel
> runs retrieving data and thought it would be both more time effective for
> me, as well as limiting the number of connections made to your MySQL
> > I am using the Core and Compara APIs and my question is, what databases
> will I need to use all the functionality of both the Core and Compara APIs?
> I assume just the core databases for Core, but would I need any others, for
> example when using the HomologyAdaptor and SytentyAdaptor in Compara?
> > Cheers,
> > Steve
> Remo Sanges - Ph.D.
> Bioinformatics - Animal Physiology and Evolution
> Stazione Zoologica Anton Dohrn
> Villa Comunale I, 80121 Napoli - Italy
> +39 081 5833428
Steve Moss, BSc (Hons)
Evolutionary Biology Group
Department of Biological Sciences
University of Hull
Hull, HU6 7RX
Evolution site: http://goo.gl/7ZReN
Personal site: http://stevemoss.ath.cx/
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