Manual installation



AskOmics work with an RDF triplestore.

Compile virtuoso or install it with docker


AskOmics is build in python3 and javascript. Install the following packages

# ubuntu
apt install -y python3 python3-venv npm
# Fedora
dnf install -y python3 python3-venv npm

Installation with scripts

Install AskOmics with and run it with AskOmics will be available at localhost:5000.

Installation with docker-compose

Clone the askomics-docker-compose repository

# clone
git clone
# cd
cd flaskomics-docker-compose/standalone
# Or, if you want to use federated queries
cd flaskomics-docker-compose/federated

Update config (see README)


sudo docker-compose up -d

AskOmics will be available at localhost.

Installation with a single docker

Docker image askomics/flaskomics-with-dependencies contain AskOmics with all his dependencies (Redis, virtuoso, celery …).

# Pull image
docker pull askomics/flaskomics-with-dependencies
# run image
docker run -d askomics/flaskomics-with-dependencies

If you need a persistent volume, run

docker run -d -v ./flaskomics-data:/tmp/flaskomics askomics/flaskomics-with-dependencies

The image create a default user at the first run. You can update this user by setting the following environment variables:

|ENV|User field|default value| |—-|—-|—-| |USER_FIRST_NAME|First name|Ad| |USER_LAST_NAME|Last name|Min| |USERNAME|Username|admin| |USER_EMAIL|Email|| |USER_PASSWORD|Password (clear)|admin| |USER_APIKEY|User api key|admin| |GALAXY_URL|Galaxy url (optional)| | |GALAXY_API_KEY|Galaxy api key (optional)| |

For example:

docker run -d -v ./flaskomics-data:/tmp/flaskomics -e USER_FIRST_NAME="John" -e USER_LAST_NAME="Wick" -e USERNAME="jwick" askomics/flaskomics-with-dependencies



Fork the AskOmics repository

then, clone your fork

git clone # replace USERNAME with your github username

Install AskOmics

Run it with dev mod

./ -d dev

AskOmics will be available at localhost:5000


Clone the askomics-docker-compose repository and go into the dev directory.

# clone
git clone
# cd
cd flaskomics-docker-compose/dev

The dev directory contain a docker-compose.yml file who can lauch all dependencies needed by AskOmics (Virtuoso, Redis, Corese, Galaxy).

# clone
docker-compose up -d

Use the ci directory to lauch dockers for testing AskOmics

cd ../ci
docker-compose up -d