To modify the location where data are stored, create .env
file executing:
./create_env.sh
Then edit properly the output .env
. Be sure to set safe user/password values.
Edit env variable CWL_DOCKER_GPUS
for setting the gpus to be used on docker container used for predictions.
N.B
Change omeseadragon:4080
in ome_seadragon.base_url and ome_seadragon.static_files_url to the local machine address.
The port is the same specified in omeseadragon-nginx service (docker-compose.omero.yaml).
./compose.sh up -d
Check if init
service exited with 0 code, otherwise restart it. It can fail for timing reason, typically sql tables do not exist yet.
To visit Airflow, go to http://localhost:<AIRFLOW_WEBSERVER_PORT>.
cd slide-importer
docker build -t slide-importer .
To import a slide, run:
. .env #docker-compose env file for airflow
docker run --rm -it -v $CWL_INPUTS_FOLDER:$CWL_INPUTS_FOLDER -v /PATH/TO/SLIDE:/upload --network deephealth-pipelines_default slide-importer --server-url http://webserver:8080 /upload/SLIDE_FILENAME --user admin
It wil prompt asking the airflow password.