[ensembl-dev] ensemb-rest setup

[Andrew Parton]

Hi Sage,

The ensembl_rest.conf file within the ensembl-rest subdirectory contains a list of parameters fed to VEP from the REST server. If you add 

dir = /path/to/cache/file

within the <Controller::VEP> section of the conf file, then VEP should be able to correctly find the cache file and run as expected. Let me know if you have any issues.

Kind Regards,
Andrew

> On 18 Aug 2020, at 21:58, Sage Hornung <sage.hornung at neogenomics.com> wrote:
> 
> Hi,
>  
> I am trying to get ensemble-rest running. I am starting with a VM provided by Ensembl. Its on Ubuntu 20.04 and it has VEP working properly. I can pass ./verify installation and have also ran a few of the test scripts successfully.
>  
> I am using the 100 Version of the API and would like to use the human assembly GRCh37
> I have pulled the latest from ensemble-rest on git and flowed the instructions found here https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development <https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development>
> I am able to get the dev server running but I get this error.
>  
> 2020/08/18 13:29:19 (1) ReturnError.pm 61> -------------------- EXCEPTION --------------------MSG: ERROR: No root_dir or dir specifiedS TACK Bio::EnsEMBL::VEP::CacheDir::new /home/ensembl/ensembl-api-folder/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:107STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache 
> 
>  
>  
>  
> I have reinstalled VEP with the script inside /VEP and added the cache files (I did resize my drive to 80GB) but I still get the error.
>  
> My guess is it has something to do with the registry. I have spent some time following the Perl files and tried setting the dir_specified in a few files manually to where my cache files were downloaded unsuccessfully.
>  
> I would greatly appreciate and help or suggestions.
>  
> Thank You,
>  
> Sage 
>  
>  
> Sage Hornung
> Software Engineer 
> 
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