[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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