[ensembl-dev] mysqldump for Macaca Fascicularis pre-data?
Jan Vogel
jan.vogel at gmail.com
Mon Dec 22 14:57:16 GMT 2014
Thanks Steve !
That's great - I'm downloading it right now. It's great to have access to it so we can start aligning some sequences …
Regards, and have a good, long, relaxing xmas break!
Jan
On Dec 22, 2014, at 3:47 PM, Steve Trevanion <steve at ebi.ac.uk> wrote:
> 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> 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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>>
>>
>>
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