[ensembl-dev] Question about updating Ensembl Perl API

[Kieron Taylor]

Hi Tung-Han.

It seems that you have only updated the ensembl-io component of the API. You must also update the core component. Are you using git to install the core API, or are you using the file here: ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz ?

ensembl-api.tar.gz contains everything you would need, such as ensembl-io as well as Core, Compara, Regulation and Variation APIs.

If you've used git to clone the core API, you will need to check out a new release branch: 

git branch
# if this says release/91 then
git pull
git checkout release/92

Once you've updated your code, you will need to be careful that your PERL5LIB contains only the correct paths for the release 92 code, or you may encounter contamination between different releases of Ensembl code.

Hope that helps,

Kieron


Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute






> On 14 May 2018, at 10:58, 張東涵 <a29644972 at gmail.com> wrote:
> 
> Hi,
> 
> I have a question about updating Ensembl Perl API. 
> 
> I used this method on ensembl website to update my ensembl Perl API  
> cd ~/src
> wget 
> https://github.com/Ensembl/ensembl-io/archive/release/92.zip
> 
> unzip 92.zip
> mv ensembl-io-release-92 ensembl-io
> 
> PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-io/modules
> export PERL5LIB
> However, I still couldn't load_registry_from_db (db_version 92)
> use Bio::EnsEMBL::Registry;
> $reg->load_registry_from_db (
>     -host => '
> ensembldb.ensembl.org
> ',
>     -user => 'anonymous',
>     -species => 'homo_sapiens',
>     -db_version => 92,
>     - verbose => '1',
> );
> 
> The warning message is 
> For homo_sapiens_core_92_38 at ensembldb.ensembl.org there is a difference in the software release (91) and the database release (92). 
> You should update one of these to ensure that your script does not crash
> 
> How can I update my Ensembl Perl API to load v92 dataset ?
> 
> Thanks
> 
> Best,
> Tung-Han .
>   
> =============================
> Tung-Han Chang, research student
> Institute of biomedical informatics , National Yang-Ming University 
> No.155, Sec.2, Linong Street, Taipei, 112 Taiwan 
> =============================
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