Configuration
The original software of EVAdb is not very configurable and does not feature
any dedicated configuration files. Therefore, the options for configuration
are very limited. Nevertheless all of the following parameters should be
set in your docker .env file prior to build time. The .env should be located
in the project root, where the docker-compose commands will be executed.
Docker .env
Make sure you understand the basics behind docker environment variables
and how the .env file fits in.
Read more: Environment variables in Compose
The following parameters are available to be configured. Please also see the example file at the end of this section.
| Setting | Description | Example |
|---|---|---|
| MYSQL_ROOT_PASSWORD | Password of the mysql root user | sup3rs3cur3 |
| MYSQL_PASSWORD | Password for the mysql user | myPass |
| MYSQL_USER | Username for the mysql account | evadb |
| MYSQL_DATABASE | Standard mysql database | solexa |
| YUBIKEY_ID | Yubikey ID (if present) | test |
| YUBIKEY_APIKEY | Yubikey api key | secr3t |
| DATABASE_DIR | Persistent database storage dir | /big_storage |
| CURRENT_UID | UID and GID to run the database with normal user permissions | 1000:1000 |
| CERT_DIR | Directory where certificates are stored | /secrets |
| INITIAL_USER | Initial evadb user name | admin |
| INITIAL_USER_PASSWD | Password for the initial evadb user | abc123 |
| ANNO_DB_DIR | Location of annotation databases (gnomAD, dbNSFP etc.) | /anno_db |
| LIBRARY | Location for library files (reference genomes etc.) | /reference |
| DATA_DIR | Directory containing data files for upload (vcf etc.) | /data |
Example .env File
Setting CURRENT_UID
To set the CURRENT_UID parameter for your own user, use the result of the command:
echo "$(id -u):$(id -g)"
The following is an example .env file. Place it in the project root directory.
MYSQL_ROOT_PASSWORD=root_pw
MYSQL_PASSWORD=user_pass
MYSQL_USER=evadb
MYSQL_DATABASE=solexa
YUBIKEY_ID=test
YUBIKEY_APIKEY=secr3t
DATABASE_DIR=/evadb
CURRENT_UID=1000:1000
CERT_DIR=/home/evadb/secrets/
INITIAL_USER=admin
INITIAL_USER_PASSWD=admin_pw
ANNO_DB_DIR=/annotation_db/
LIBRARY=/library/
DATA_DIR=/data/