Environment Configuration
OpenGenomeBrowser relies on Docker environment variables for configuration, enabling flexible setup across different environments. Use the configuration provided in the Docker template to get started, and customize these settings as needed with docker compose -f <var.env> up.
OpenGenomeBrowser Settings
| Variable |
Description |
Default Value |
Required |
PROTEIN_FASTA_ENDINGS |
Sets the file extension expected for protein FASTA files. |
faa |
No |
DEFAULT_ANNOTATION_TYPE |
Defines the annotation type used as the default for the application. |
OL |
No |
ORTHOFINDER_ENABLED |
Enables OrthoFinder for ortholog analysis. |
false |
No |
CLUSTALO_ENABLED |
Enables Clustal Omega for sequence alignment. |
false |
No |
IQTREE_ENABLED |
Enables IQ-TREE for phylogenetic inference. |
false |
No |
RAXML_ENABLED |
Enables RAxML-ng for phylogenetic analysis. |
false |
No |
LOGIN_MESSAGE |
Customizable login message, e.g., "Welcome to the OpenGenomeBrowser demo server!". |
None |
No |
DEFAULT_GENOMES_TABLE_URL |
Defines filter parameters for the genomes table. |
None |
No |
System Settings
| Variable |
Description |
Default Value |
Required |
USER_ID |
Numeric ID for the user running the application. |
None |
Yes |
GROUP_ID |
Numeric ID for the user’s group. |
None |
Yes |
DEBUG |
Toggles Django’s debug mode. |
false |
Yes |
LOG_LEVEL |
Configures logging verbosity. |
INFO |
No |
DJANGO_SECRET_KEY |
Secret key for Django’s cryptographic signing. |
None |
Yes |
DJANGO_ALLOWED_HOSTS |
Comma-separated list of hostnames or IPs allowed to access the app. |
None |
Yes |
LOGIN_REQUIRED |
Enforces login for accessing the application when set to true. |
false |
No |
UWSGI_WORKERS |
Specifies the number of uWSGI workers for handling requests. |
5 |
No |
HUEY_WORKERS |
Sets the number of workers for the Huey task queue. |
None |
No |
HARAKIRI |
Specifies uWSGI’s request timeout in seconds. |
None |
No |
Cache Settings
| Variable |
Description |
Default Value |
Required |
CACHE_DIR |
Directory path for storing cached data. |
/tmp/ogb-cache |
No |
CACHE_MAXSIZE |
Maximum cache size in MB. |
20 |
No |
PostgreSQL Database Settings
| Variable |
Description |
Default Value |
Required |
DB_HOST |
Database hostname. |
db |
Yes |
DB_PORT |
Database port. |
5432 |
Yes |
DB_NAME |
Name of the PostgreSQL database. |
None |
Yes |
DB_USER |
Username for the database. |
None |
Yes |
DB_PASSWORD |
Password for database authentication. |
None |
Yes |
Email Settings
| Variable |
Description |
Default Value |
Required |
EMAIL_HOST |
SMTP server used for sending email notifications. |
None |
No |
EMAIL_HOST_USER |
Username for SMTP authentication. |
None |
No |
DEFAULT_FROM_EMAIL |
Default sender email address for outgoing messages. |
None |
No |
EMAIL_PORT |
SMTP server port. |
None |
No |
This format separates the settings into their respective sections with tables for better readability and organization.
This configuration allows you to quickly tune environment-specific settings for development, testing, and production, with optional variables for additional functionality. Ensure all required fields are populated, especially in production environments.