[ensembl-dev] mysqldump for Macaca Fascicularis pre-data?

[Steve Trevanion]

Hi Jan,

Sorry for the delay. I have a MySQL dump of the 75 schema database and 
have put it, gift wrapped, on the Pre! FTP site 
(ftp://ftp.ensembl.org/pub/pre/mysql/75/pre_macaca_fascicularis_core_75_1).

I can't comment on the genebuilders plans for this species

Cheers,

Steve

On 21/12/14 22:21, Jan Vogel wrote:
>
> Hi Anne and EnsEMBLers,
>
> I haven't heard back from you guys for a while … but it could well be 
> that I missed the email with more details.
>
> Is there a slight chance that the data dump could be provided before 
> the holidays,  as kind of like an end-of-the-year present for us ?
> Doesn't have to be wrapped :-)
>
> Jan
>
>
> On Oct 9, 2014, at 5:10 AM, Jan Vogel <jan.vogel at gmail.com 
> <mailto:jan.vogel at gmail.com>> wrote:
>
>> Hello Anne,
>>
>> a dump would be great. If you don't have a site / location, I can 
>> send you my dropbox link.
>> we could also use the Max-Planck-Institute websafe 
>> https://ws.molgen.mpg.de/cgi-bin/websafe for exchange.
>>
>> Thanks again,
>>
>>    Jan
>>
>>
>>
>> On Tue, Oct 7, 2014 at 4:32 AM, Anne Lyle <annelyle at ebi.ac.uk 
>> <mailto:annelyle at ebi.ac.uk>> wrote:
>>
>>     Hi Jan
>>
>>     You’re right that not all data is provided for “pre” species -
>>     we’ve started producing the basic FASTA files (DNA, cDNA, etc) as
>>     a matter of routine but that’s about it. I’ll have a look at
>>     sorting out a MySQL dump for you, though.
>>
>>     As for plans, I’ll have to leave that up to the genebuilders to
>>     comment on.
>>
>>     Regards
>>
>>     Anne
>>
>>
>>
>>     Anne Lyle
>>     Ensembl Web Developer
>>     European Bioinformatics Institute (EMBL-EBI)
>>     East Wing, A3-118, Wellcome Trust Genome Campus, Hinxton,
>>     Cambridge, UK
>>
>>     Phone: +44 (0)1223 494178 <tel:%2B44%20%280%291223%20494178>
>>     Email: annelyle at ebi.ac.uk <mailto:annelyle at ebi.ac.uk>
>>     Web: www.ensembl.org <http://www.ensembl.org/>
>>
>>
>>
>>
>>
>>     On 6 Oct 2014, at 19:03, Jan Vogel <jan.vogel at gmail.com
>>     <mailto:jan.vogel at gmail.com>> wrote:
>>
>>>
>>>     Hello Ensembl,
>>>
>>>     I've seen that the crab-eating macaque assembly is up in
>>>     pre.ensembl.org <http://pre.ensembl.org/>, based on MacFas5.0:
>>>
>>>     http://pre.ensembl.org/Macaca_fascicularis/Info/Index/
>>>
>>>     This is great, as I'm really interested in this organism and I
>>>     like to work it.
>>>
>>>     I'm looking for the mysql dump for Macaca Fascicularis so I can
>>>     re-create the core database in m own environment - however, I
>>>     did not find anything on the usual FTP server:
>>>
>>>     ftp://ftp.ensembl.org/pub/pre/gtf/macaca_fascicularis/
>>>
>>>     I also couldn't find the pre-db on the public mysql server….
>>>
>>>     Any chance ensembl can provide this data ? Or does it exist and
>>>     i just didn't find it ?
>>>
>>>     I'm aware that this is  an ensembl pre-build, that not all
>>>     standard data is available and this is all just "early-access".
>>>
>>>     On a different note, it would also be great to know what the
>>>     general plans with this species are - Is Ensembl planning on a
>>>     full build or a projection build ? And is there a rough date
>>>     when such a build will be released ?
>>>
>>>     Thanks,
>>>
>>>        Jan Vogel
>>>     _______________________________________________
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>>
>>
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>
>
>
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