[ensembl-dev] Problem with VEP

Andy Yates ayates at ebi.ac.uk
Sat Nov 19 16:15:38 GMT 2011


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
>>> 
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe):
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>> 
>> 
>> 
>> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

---
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/





More information about the Dev mailing list