In production, AskOmics is deployed with docker and docker-compose. We provide docker-compose.yml templates to deploy your instance.


Install git

# Debian/Ubuntu
apt install -y git
# Fedora
dnf install -y git

Install docker:

Install docker-compose:

# Debian/Ubuntu
apt install -y docker-compose
# Fedora
dnf install -y docker-compose


Download templates

First, clone the flaskomics-docker-compose repository. It contain template files to deploy your AskOmics instance.

git clone

This repo contains several directories, depending on your needs

cd flaskomics-docker-compose
ls -1

Two directories are used for production deployment

  • standalone: deploy AskOmics with all its dependencies for a standalone usage
  • federated: deploy AskOmics with all its dependencies and a federated query engine for a federated usage (Cross external endpoint such as NeXtProt with local data)

Choose one of this directory depending of your needs

cd federated


First, edit the docker-compose.yml file. You can change the main port:

  • services > nginx > ports: You can change the default port if 80 is already used on your machine. Example: "8080:80" to use 8080 instead of 80.


Then, configure virtuoso by editing virtuoso.env

Edit VIRT_Parameters_NumberOfBuffers and VIRT_Parameters_MaxDirtyBuffers following rules described here.


Change the DBA_PASSWORD if you plan to expose the virtuoso endpoint. The password endpoint have to be the same in askomics.env > ASKO_triplestore_password

Nginx (web proxy)

Nginx is used to manage web redirection. Nginx configuration is in two files: nginx.conf and nginx.env. If you want to access the virtuoso endpoint, uncomment the virtuoso section in nginx.conf


All properties defined in askomics.ini can be configured via the environment variables in askomics.env. The environment variable should be prefixed with ASKO_ and have a format like ASKO_$SECTION_$KEY. $SECTION and $KEY are case sensitive. E.g. property footer_message in the askomics section should be configured as ASKO_askomics_footer_message=Welcome to my AskOmics!.


Change ASKO_flask_secret_key and ASKO_askomics_password_salt to random string

For more information about AskOmics configuration, see configuration section.

First user

environment variables can also be used to create a user into AskOmics at first start. For this, use CREATE_USER=true User information can be configured with the following environment variables:

  • USER_FIRST_NAME: User first name (default: Ad)
  • USER_LAST_NAME: User last name (default: Min)
  • USER_USERNAME: Username (default: admin)
  • USER_PASSWORD: Password (default: admin)
  • USER_EMAIL: User email (default:
  • USER_APIKEY: User API key (default: admin)
  • GALAXY_API_KEY: Galaxy URL linked to the user (optional)
  • GALAXY_URL: User Galaxy API Key (optional)

The user will be created only if the users table of the database is empty.