How to enable the eQTL endpoint

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Magali Ruffier edited this page Mar 12, 2018 · 2 revisions

Install HDF5

https://support.hdfgroup.org/HDF5/ Ensembl currently uses 1.10, but also work with 1.8

Compile ensembl-hdf5

Please follow the instructions here: https://github.com/ensembl/ensembl-hdf5

Download the hdf5 database containing the GTEx data (2 files)

ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/eqtl/

Edit the <eqtl_dbs> tag in ensembl-rest/ensembl-rest.conf

<Model::Registry>

[...]

preload = 1

# Location of HDF5/SQLite DBs if EQTL endpoint is used

<eqtl_dbs>

    human = /path/to/GTEx.V6.88_38.cis.eqtls.h5

</eqtl_dbs>

</Model::Registry>

(Re-)start the REST server

REST API | Ensembl