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

[Sergei Manakov]

Thanks Pual, the problem was indeed with the & symbols in my wget
commands. With the correct syntax API matches the database version
perfectly.

thanks,
Sergei


On 8 January 2012 15:27, Paul Flicek <flicek at ebi.ac.uk> wrote:
> 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
>>>
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>>
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>