[ensembl-dev] mysqldump for Macaca Fascicularis pre-data?
Thibaut Hourlier
thibaut at ebi.ac.uk
Tue Jan 6 15:32:49 GMT 2015
Hi Jan,
Sorry for the delay, we have plans to annotate the crab-eating macaque, unfortunately we don't have an estimation of a release date at the moment.
Regards
Thibaut
On 22 Dec 2014, at 14:57, Jan Vogel <jan.vogel at gmail.com> wrote:
> 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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