ensembl-rest-docker

Docker container for setting up an Ensembl REST server

Checkout this git repository:

git clone https://github.com/duartemolha/ensembl-rest-docker.git

cd ensembl-rest-docker

To build your image you can use one of the ready made .env_ensembl files contained in "connection_conf_files" folder or create one of your own contaning the same arguments I.e. Rename one of the 2 connection_conf_files/.env.ensembl_grch38 or connection_conf_files/.env.ensembl_grch37 files to .env_custom and modify its contents if you want to connect to a different server. Currently they are set with the default ensembl settings and targeting API release 109

Build the docker image:

bash build.sh \
    --build-name [name_of_container (default: ensembl-rest)] \
    --env-file [env file (required)]

# for example you could just use the ready made template file to create a rest server for GRCh38 as such:
bash build.sh \
    --build-name ensembl-rest-grch38 \
    --env-file connection_conf_files/.env.ensembl_grch38

Run docker container, specifing the expose port on your host machine where the server will be accessed:

docker run -d --name [build_name] -p 3000:80 [build_name]
# using default parameters this would be:
docker run -d --name ensembl-rest -p 8080:80 ensembl-rest

Test by visiting the port that the docker container was started on:

curl 'localhost:8080/lookup/id/ENSG00000157764?' -H 'Content-type:application/json'

Result:

{   "db_type":"core",
    "strand":-1,
    "start":140719327,
    "source":"ensembl_havana",
    "biotype":"protein_coding",
    "assembly_name":"GRCh38",
    "id":"ENSG00000157764",
    "object_type":"Gene",
    "species":"homo_sapiens",
    "display_name":"BRAF",
    "end":140924929,
    "version":14,
    "description":"B-Raf proto-oncogene, serine/threonine kinase [Source:HGNC Symbol;Acc:HGNC:1097]",
    "logic_name":"ensembl_havana_gene_homo_sapiens",
    "seq_region_name":"7"
}