[ensembl-dev] ensemb-rest setup
aparton at ebi.ac.uk
Wed Aug 19 10:48:03 BST 2020
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.
> On 18 Aug 2020, at 21:58, Sage Hornung <sage.hornung at neogenomics.com> wrote:
> 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 Hornung
> Software Engineer
> NeoGenomics Laboratories, Inc.
> 2131 Faraday Avenue, Carlsbad, CA 92008
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