caMicroscope Deployment/Installation Guide

 

caMicroscope Docker Distribution

Architecture

• Application => Viewer
• Data => Data
• Backend => Loader

Installation

Build images

• docker build -t camicroscope_data data/
• docker build -t camicroscope_loaders loaders/
• docker build -t camicroscope_viewer viewer/

These builds take about an hour, so feel free to grab a coffee. 

Running the containers

Data

1. Set environment variables on host machine for Images and Data directories export CAMIC_IMAGES_DIR=<path to images directory> export CAMIC_DATA_DIR=<path to data directory>
2. Set Bindaas port $CAMIC_BINDAAS_PORT=9099
docker run -itd -p $CAMIC_BINDAAS_PORT:9099 -v $CAMIC_IMAGES_DIR:/data/images -v $CAMIC_DATA_DIR:/data/db camicroscope_data
3. Run docker inspect to find the IP address for Data container.
4. Use <CAMIC_DATA_IP> as a placeholder.

Loaders

1. Set up environment variables:
$CAMIC_KUE_PORT=5000
$CAMIC_MARKUPLOADER_PORT=6000
$CAMIC_DATALOADER_PORT=6002


2. Run the container:
docker run -itd -p $CAMIC_KUE_PORT:3000 -p $CAMIC_MARKUPLOADER_PORT:3001 -p $CAMIC_DATALOADER_PORT:3002 -v $CAMIC_IMAGES_DIR:/data/images -e "dataloader_host=http://<CAMIC_DATA_IP>:9099" -e "annotations_host=http://<CAMIC_DATA_IP>:9099" camicroscope_loaders

Note that -p $CAMIC_KUE_PORT:3000 -p $CAMIC_MARKUPLOADER_PORT:3001 -p $CAMIC_DATALOADER_PORT:3002 is optional.

Viewer

1. Set up environment variables:
$CAMIC_VIEWER_PORT=1337
<HTML_DIRECTORY> is /viewer/html. Provide the absolute path.
   
   
2. Run:
docker run -itd -p $CAMIC_VIEWER_PORT:80 -v <HTML_DIRECTORY>/html:/var/www/html -v $CAMIC_IMAGES_DIR:/data/images camicroscope_viewer

You should now be able to load the images and see them at http://localhost:$CAMIC_VIEWER_PORT/camicroscope2/osdCamicroscope.php?tissueId=<Case_ID>