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[ARCHIVE] caMicroscope Docker Distribution Guide

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Ryan Birmingham edited this page Mar 29, 2020 · 1 revision

This page is severely out of date. Please see https://github.com/camicroscope/distro

Goal of this guide

The goal of this guide is to be able to install all of caMicroscope componenets using docker containers. This guide will also guide you how to upload an image, its markups and see them in caMicroscope viewer.

Architecture

camicroscope architecture

Requirements

Please make sure you have docker and git installed.

Building container images

Clone all docker images

  • git clone https://github.com/camicroscope/DataDockerContainer
  • git clone https://github.com/camicroscope/LoaderDockerContainer
  • git clone https://github.com/camicroscope/ViewerDockerContainer

Build the docker images

  • docker build -t camicroscope_data DataDockerContainer
  • docker build -t camicroscope_loader LoaderDockerContainer
  • docker build -t camicroscope_viewer ViewerDockerContainer

Running docker containers

  • ./install.sh will run the 3 containers in default configuration

Configuring viewer to use Data container.

Edit /var/www/html/camicroscope2/api/Configuration/config.php to set the $baseUrl to the IP of dataDockerContainer.

Loading image

Lets assume you have an image TCGA-A1-A0SD-01A-01-BS1.svs on your file system. To view this image in caMicroscope you'll need to load the image through caMicroscope data loader.

Post Image

curl -v -F case_id=TCGA-A1-A0SD -F [email protected] http://localhost:6002/submitData or go to http://localhost:6002 in your browser to use the uploader UI. You should get a success message.

Viewing image

Open http://localhost:1337/camicroscope2/osdCamicroscope.php?tissueId=TCGA-A1-A0SD to view the image. Please note the tissueId parameter is the case_id you supplied while loading the image

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