[ensembl-dev] ensemb-rest setup

Sage Hornung sage.hornung at neogenomics.com
Tue Aug 18 21:58:27 BST 2020


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
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
Phone: 760.516.5114
Cell: 760.755.3930
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