genetics-backend

QC, spin VMs, load data into DBs, create LUTs and other fun backend stuff we need to do to spin https://genetics.opentargets.io

Dockerfile

There is a docker file to create an image with the project and required dependencies in place.

How to run the docker container

Build image and tag it with a name for convenience of calling later:

    docker build --tag otg-etl .

Use the Google Cloud Storage as source to load release data

Start a docker container in interactive mode.

Host names must not contain protocol (https is assumed) or slashes. The data loading script uses localhost if no host name provided.

    docker run -it --rm \
    --env ES_HOST='<elasticsearch host name>' \
    --env CLICKHOUSE_HOST='<ot clickhouse db host name>' \
    otg-etl

Authenticate google cloud storage.

    gcloud auth application-default login

Load release data to ot database and the Elasticserch.

    bash genetics-backend/loaders/clickhouse/create_and_load_everything_from_scratch.sh gs://genetics-portal-output/190504

Use local disk as source to load release data

Start a docker container in interactive mode.

Host names must not contain protocol (https is assumed) or slashes. The data loading script uses localhost if no host name provided.

    docker run -it --rm \
    --env ES_HOST='<elasticsearch host name>' \
    --env CLICKHOUSE_HOST='<ot clickhouse db host name>' \
    -v <directory with data>:/data/
    otg-etl

Load release data to ot database and the Elasticserch.

    bash genetics-backend/loaders/clickhouse/create_and_load_everything_from_scratch.sh /data

Download release data from FTP to local file system

You can use wget to download the release data. Below is an example of the command for 19.05.04 release data.

    wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/190504/