|
|
|
1. Install HDF5
|
|
|
|
|
|
|
|
https://support.hdfgroup.org/HDF5/
|
|
|
|
Ensembl currently uses 1.10, but also work with 1.8
|
|
|
|
|
|
|
|
2. Compile ensembl-hdf5
|
|
|
|
|
|
|
|
Please follow the instructions here:
|
|
|
|
https://github.com/ensembl/ensembl-hdf5
|
|
|
|
|
|
|
|
3. Download the hdf5 database containing the GTEx data (2 files)
|
|
|
|
|
|
|
|
ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/eqtl/
|
|
|
|
|
|
|
|
4. 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>
|
|
|
|
|
|
|
|
5. (Re-)start the REST server |
|
|
\ No newline at end of file |
