[ensembl-dev] database model and API versions

[mag]

Hi Duarte,

The mysql dumps for GRCh37 are available on the ftp site as well
ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/

I would recommend having only one copy of human for release 79.
So if you are interested in the GRCh37 data, you can download the 
database from ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/ rather 
than ftp://ftp.ensembl.org/pub/release-79/mysql/

If you need both databases on the same server, you can access a given 
database directly rather than using the registry.
my $human_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
     -HOST => 'localhost',
     -PORT => 3306,
     -USER => 'user',
     -DBNAME => 'homo_sapiens_core_79_37',
     -SPECIES => 'homo_sapiens',
     -GROUP => 'core'
);


Hope that helps,
Magali

On 27/04/2015 17:11, Duarte Molha wrote:
> Thanks Magali
>
> But I think you have not understtod my question.
>
> Assume I want to download the databases to my local computer and use 
> the perl API 79 to query the latest 79_37 database instead of the 
> default 79_38.
> Previously, I just had to download the mysql tables corresponding to 
> the api I was using to fetch the data correctly, however, now you have 
> broken that link API->Underlying_assembly
>
> So how do I tell my scripts what database to query?
>
> My local sql will all be under the same port.
>
> Best regards
>
> Duarte
>
>
>
> =========================
>      Duarte Miguel Paulo Molha
> http://about.me/duarte
> =========================
>
> On 27 April 2015 at 17:01, mag <mr6 at ebi.ac.uk <mailto:mr6 at ebi.ac.uk>> 
> wrote:
>
>     Hi Duarte,
>
>     The archive 75 website is still based on the release 75 API.
>
>     For the dedicated GRCh37 website though, we have used a data
>     freeze from release 75 and have since been updating the website
>     and underlying databases along with the main release.
>     The GRCh37 databases are available on our main MySQL server on
>     port 3337 (instead of the default 3306 which will give you access
>     to GRCh38 databases)
>
>
>     Hope that helps,
>     Magali
>
>
>     On 27/04/2015 16:56, Duarte Molha wrote:
>>     Dear developers
>>
>>     On your GRCh37 archive site you say this:
>>
>>     ===========================
>>
>>
>>         About this archive
>>
>>     This archive is based on Ensembl Release 75 data, and gives
>>     continuing access to human assembly GRCh37, as well as all our
>>     other release 75 species (data freeze March 2014) for comparative
>>     purposes. Human variation and regulation data has since been
>>     updated in March 2015.
>>
>>     The API and website will be updated in tandem with the release of
>>     the main Ensembl website (*currently version 79*), and we will
>>     also periodically update this site with new data human, which
>>     will be announced in this panel.
>>
>>     MySQL dumps of human databases on the most recent schema version
>>     are available on ourFTP site <ftp://ftp.ensembl.org/pub/grch37/>.
>>
>>     =========================
>>
>>     It was my understanding that an API version was directly linked
>>     to a specific assembly. So I thought that if I wanted to query
>>     the latest GRCh37 assembly I would need to use the api v75 and if
>>     I wanted to use a local database, I would download the
>>     corresponding sql tables for that version.
>>
>>     However, according to this announcement, I can now use the V79
>>     api and query the old assembly... How is this accomplished ?
>>     What you I have to do on my scripts to make sure I am querying
>>     the 37 version even though I am using the latest API?
>>
>>     Sorry, I hope this is not a stupid question but I am a bit confused.
>>
>>     Best regards
>>
>>     Duarte
>>
>>
>>
>>     =========================
>>          Duarte Miguel Paulo Molha
>>     http://about.me/duarte
>>     =========================
>>
>>
>>     _______________________________________________
>>     Dev mailing listDev at ensembl.org  <mailto:Dev at ensembl.org>
>>     Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>     Ensembl Blog:http://www.ensembl.info/
>
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150427/33324f54/attachment.html>