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STOP-HCV LabKey Database Application Container

This repository contains docker and installation files in order to set up the LabKey database components required to provide a LabKey Server installation LabKey Server in Docker.

Components

The database Docker image is based on the postgres:9.6 image from Docker Hub repository.

The Postgres version used 9.6, which is based on the debian:jessie Docker image.

To build the lkey_userdb docker image use the following command from within the labkey_db directory.

docker build -t lkey_userdb .

To run up the labkey user db component use the following command:

docker run -d --network labkey_net --name lkey_userdb lkey_userdb

The username and password configured for the lkey_userdb must correspond for the lkey_userdb and labkey_core containers.

-----------------------------------------------------------------------------------------------------
|Item                | Container | Defined in           | Variable Name   | Default Value           |
-----------------------------------------------------------------------------------------------------
|lkey_userdb username|labkey_core|labkey_core/Dockerfile|LKDB_USER        |'postgres'               |
|lkey_userdb password|labkey_core|labkey_core/Dockerfile|LKDB_PASSWORD    |'passwordForLabkeyUserDb'|
|lkey_userdb username|lkey_userdb|lkey_userdb/Dockerfile|POSTGRES_USER    |'postgres'               |
|lkey_userdb password|lkey_userdb|lkey_userdb/Dockerfile|POSTGRES_PASSWORD|'passwordForLabkeyUserDb'|
-----------------------------------------------------------------------------------------------------

To override these values when invoking the lkey_userdb docker image use the following command.

docker run -d --network labkey_net \
           --name lkey_userdb \
           -e POSTGRES_PASSWORD=newPasswordForLabKeyDb \
           -e POSTGRES_USER=newUsernameForLabKeyDb \
           lkey_userdb

For the STOP-HCV project a second database containing the clinical, viral sequencing and host genotyping data is also required.

To run up the labkey user db component use the following command:

A string substitution appears to be made by the application on the hostname in the labkey.xml file which results in the application being unable to find the host. e.g. a host name of 'lkey_userdb' works, whereas 'labkey_userdb' does not.

Infrastructure

In order for the various Docker containers created above to be able to talk to each other a docker network needs to be created. The name used in all examples is 'labkey_net'.

docker network create labkey_net

Support

If you need support using these docker builds, please contact: