[ensembl-dev] Setup ensembl in local system

Brandon Walts bwalts at ebi.ac.uk
Fri Jul 30 17:14:39 BST 2021


Hello Chanchal Sen

Instead of installing the entire REST API, you might want to investigate the VEP command-line tool ( https://www.ensembl.org/info/docs/tools/vep/script/index.html <https://www.ensembl.org/info/docs/tools/vep/script/index.html> ) to see if it would be faster for your queries without the complexity of a full REST API install. The VEP command line tool is also available as a Docker image.

If you decide to install the full REST API, you can find instructions for installing your own copy at https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development <https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development> - hopefully this provides enough detail to be helpful.
The REST API depends upon the Ensembl Perl API. Instructions for installing the Perl API are linked from the REST API installation instructions. These instructions list the specific repos that you will need to clone from GitHub.

Both the VEP command-line tool and the REST API require database connections. If you would like to install your own local copy, a “core” database for your species of interest should be sufficient, unless you plan to query for co-located variants, or use SIFT or PolyPhen. For Homo sapiens GRCh37, a dump of the current core database can be downloaded at http://ftp.ensembl.org/pub/grch37/release-104/mysql/homo_sapiens_core_104_37/ <http://ftp.ensembl.org/pub/grch37/release-104/mysql/homo_sapiens_core_104_37/> - within that directory you will find a .sql file describing the schema and .txt files containing the data. For Homo sapiens GRCh38, the database can be downloaded at http://ftp.ensembl.org/pub/current_mysql/homo_sapiens_core_104_38/ <http://ftp.ensembl.org/pub/current_mysql/homo_sapiens_core_104_38/> . Step by step instructions for loading a MySQL database from these files are here: https://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html <https://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html>

For the REST API, you should edit the ensembl_rest.conf file to point to your local database installation. For the VEP command-line tool, you should edit the Ensembl “registry” file to point to your local database installation as described at https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#database <https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#database>

These two email threads from the ensembl-dev list may be helpful for configuring the HGVS endpoint and VEP Cache installation for the REST API: https://lists.ensembl.org/pipermail/dev_ensembl.org/2020-September/000460.html <https://lists.ensembl.org/pipermail/dev_ensembl.org/2020-September/000460.html> and https://lists.ensembl.org/pipermail/dev_ensembl.org/2020-August/000445.html <https://lists.ensembl.org/pipermail/dev_ensembl.org/2020-August/000445.html>

Kind regards
Brandon Walts - Ensembl Infrastructure team

> On 29 Jul 2021, at 10:21, Chanchal Sen <chanchalsen.it at gmail.com> wrote:
> 
> Hi Team,
> 
> Currently, I am using the below API for fetching responses.
> http://grch37.rest.ensembl.org/vep/human/hgvs/NF1:p.K1457E <http://grch37.rest.ensembl.org/vep/human/hgvs/NF1:p.K1457E>
> http://rest.ensembl.org/vep/human/hgvs/NF1:p.K1457E <http://rest.ensembl.org/vep/human/hgvs/NF1:p.K1457E>
> 
> But this sometimes takes time and I wish to set up an on-premise database in my local system.
> 
> I am using a mac and referring to the below sections in the website, but this is kind of generic and has so many repo under git "https://github.com/Ensembl <https://github.com/Ensembl>" and a list of databases under "http://grch37.ensembl.org/info/data/ftp/index.html <http://grch37.ensembl.org/info/data/ftp/index.html>". 
> 
> So, request you to please guide me on which exact repo to refer to in git and which databases to download that can help get a response for the above two API's.
> 
> Regards,
> Chanchal
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