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

[Jan Vogel]

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> 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> 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
> Email: annelyle at ebi.ac.uk
> Web: www.ensembl.org
> 
> 
> 
> 
> 
> On 6 Oct 2014, at 19:03, Jan Vogel <jan.vogel at gmail.com> wrote:
> 
>> 
>> Hello Ensembl, 
>> 
>> I've seen that the crab-eating macaque assembly is up in 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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