[ensembl-dev] Problem with VEP

[Ivan Smirnov]

Thanks Andy,

you may be right, I was using a little bash script to automate the process:

#!/bin/bash
V=64
U=http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi
for API in ensembl ensembl-compara ensembl-variation ensembl-functgenomics
do
   wget -O $API.tar.gz
"$U/$API.tar.gz?root=ensembl&only_with_tag=branch-ensembl-${V}&view=tar"
done

The funny thing the same script downloads the correct version today...

Ivan

On Sat, Nov 19, 2011 at 8:15 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> Hi Ivan,
>
> The links on the API installation page do point to v64 but I think you may have encountered an issue when using these links in the unix terminal. Since the URLs contain the & character most shells will interpret this as you wanting the fork the download. So even though you may have requested:
>
> wget http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-64&view=tar
>
> The command is interpreted as
>
> wget http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz
>
> To get around this surround the URL in single quotes i.e.
>
> wget 'http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-64&view=tar'
>
> All the best,
>
> Andy
>
> p.s. I believe the other issue you were referring to was an issue with the API dump at ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz which at one point was a corrupted version of 64. This has been fixed & was last updated on the 14th November.
>
> On 19 Nov 2011, at 06:35, Ivan Smirnov wrote:
>
>> Hi Daniel,
>>
>> I used the links from the page
>> http://www.ensembl.org/info/docs/api/api_installation.html. They do
>> point to version 64, but actual tar.gz files are sent back for version
>> 65. This issue was already pointed in October, but was never fixed.
>> Anyway, I am glad that at CVS installation works correctly.
>>
>> Thanks
>> Ivan
>>
>> On Fri, Nov 18, 2011 at 5:11 PM,  <sobral at ebi.ac.uk> wrote:
>>> You seem to have an incorrect instalation of the API.
>>> You probably installed from the HEAD code instead of the release branch.
>>> The HEAD code is already pointing to the future databases of release 65
>>> (out in early December).
>>>
>>> You need to install it as described here:
>>> http://www.ensembl.org/info/docs/api/api_cvs.html
>>>
>>> Hope this helps.
>>> Daniel
>>>
>>>
>>>> I have downloaded latest API and variant_effect_predictor.pl (v.2.2),
>>>> and when I try to run it I am getting errors:
>>>>
>>>> -------------------- WARNING ----------------------
>>>> MSG: homo_sapiens is not a valid species name (check DB and API version)
>>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1159
>>>> CALLED BY: ./variant_effect_predictor.pl  LINE: 462
>>>> Ensembl API version = 65
>>>> ---------------------------------------------------
>>>>
>>>> -------------------- WARNING ----------------------
>>>> MSG: homo_sapiens is not a valid species name (check DB and API version)
>>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1159
>>>> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 953
>>>> Ensembl API version = 65
>>>> ---------------------------------------------------
>>>>
>>>> -------------------- EXCEPTION --------------------
>>>> MSG: Can not find internal name for species 'homo_sapiens'
>>>> STACK Bio::EnsEMBL::Registry::get_adaptor
>>>> /home/isadmin/arch/Perl/ensembl/modules/Bio/EnsEMBL/Registry.pm:955
>>>> STACK main::get_adaptors ./variant_effect_predictor.pl:707
>>>> STACK main::configure ./variant_effect_predictor.pl:559
>>>> STACK toplevel ./variant_effect_predictor.pl:61
>>>> Ensembl API version = 65
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> Another strange thing is that when I was downloading API the link says
>>>> version 64, as in:
>>>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-64&view=tar
>>>> but from the error message it seems that the version is 65??
>>>>
>>>> Help!
>>>> Ivan
>>>>
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>>>>
>>>
>>>
>>>
>>
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>
> ---
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
>
>