crs4 / deephealth-pipelines

DeepHealth Pipelines

Configure

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).

Deploy

./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>.

Upload data

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.