Deployment¶
User¶
Manual installation¶
Dependencies¶
Python3/venv/npm¶
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 install.sh and run it with run_all.sh. AskOmics will be available at localhost:5000.
Installation with docker-compose¶
Clone the askomics-docker-compose repository
# clone
git clone https://github.com/askomics/flaskomics-docker-compose.git
# cd
cd flaskomics-docker-compose
Update config (see README)
Run
sudo docker-compose up -d
AskOmics will be available at localhost.
Installation with a single docker¶
Docker image askomics/full-flaskomics contain AskOmics with all his dependencies (Redis, virtuoso, celery …).
# Pull image
docker pull askomics/full-flaskomics
# run image
docker run -d askomics/full-flaskomics
If you need a persistent volume, run
docker run -d -v ./flaskomics-data:/tmp/flaskomics askomics/full-flaskomics
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|admin@example.org|
|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/full-flaskomics
Developer¶
Fork the AskOmics repository
then, clone your fork
git clone https://github.com/USERNAME/flaskomics.git # replace USERNAME with your github username
Run it with dev mod
./run_all.sh -d dev
AskOmics will be available at localhost:5000