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How to enable the eQTL endpoint
Magali Ruffier edited this page Mar 12, 2018
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- 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