[ensembl-dev] Is Perl API already version 66?

[Paul Flicek]

Hi Sergei,

If you are using wget you have to escape the ampersands in the URL or you will cut off the part of the command that specifies the tag.


Paul


On 8 Jan 2012, at 23:20, Sergei Manakov wrote:

> Hi Bert,
> 
> I just copied links from
> http://uswest.ensembl.org/info/docs/api/api_installation.html and
> downloaded them with wget.
> 
> Is this not a good way of downloading the Perl API?
> 
> thanks,
> Sergei
> 
> 
> 
> On 8 January 2012 14:58, Bert Overduin <bert at ebi.ac.uk> wrote:
>> Hello Sergei,
>> 
>> I suspect you have downloaded the head code instead of the 65 branch ....
>> 
>> Cheers,
>> Bert
>> 
>> On Sun, Jan 8, 2012 at 10:30 PM, Sergei Manakov <manakov at ebi.ac.uk> wrote:
>>> Hello,
>>> 
>>> I downloaded new API from ensembl website yesterday, and it appears to
>>> be of version 66.
>>> 
>>> I load registry like that:
>>> 
>>> my $registry = 'Bio::EnsEMBL::Registry';
>>> $registry->load_registry_from_db(
>>>  '-host'       => 'ensembldb.ensembl.org',
>>>  '-user'       => 'anonymous',
>>>  '-db_version' => '65'
>>> );
>>> 
>>> I get this warning: "For mus_musculus_core_65_37 there is a difference in the
>>> software release (66) and the database release (65). You should update
>>> one of these to ensure that your script does not crash."
>>> 
>>> And if I change '-db_version' => '66' the the script crashes saying:
>>> "MSG: Mouse is not a valid species name (check DB and API version)".
>>> Clearly, "Mouse" is a valid species name, so I assume that Ensembl 66
>>> is not ready yet.
>>> 
>>> If you know where the problem might be, please let me know.
>>> 
>>> thanks,
>>> Sergei
>>> 
>>> _______________________________________________
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>> 
>> 
>> 
>> --
>> Bert Overduin, Ph.D.
>> Vertebrate Genomics Team
>> 
>> EMBL - European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge CB10 1SD
>> United Kingdom
>> 
>> http://www.ebi.ac.uk/~bert
>> 
>> Ensembl browser: http://www.ensembl.org
>> 
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>> 
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>> 
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> 
> _______________________________________________
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