CytoExploreR-Docker

Dillon Hammill 2023-03-10

Docker development environment for CytoExploreR Version 2.0.0

This repository contains a dockerfile and associated build instructions to launch a CytoExploreR v2.0.0 RStudio environment for testing, development or benchmarking.

The pre-built docker images are available for download (amd64 platform) from docker hub: docker pull dhammill/cytoexplorer-devel:v2.0.0.

This docker image contains:

1. Ubuntu 18.04
2. FFTW
3. FIt-SNE executable
4. Open-source cytoverse packages
5. CytoExploreRData datasets
6. CytoExploreR
7. tidyverse packages

Build Docker image locally

1. Clone this repository to obtain a local copy: git clone https://github.com/djhammill/CytoExploreR-Docker.git

2. From the terminal/command prompt build and tag the docker image: docker build -t cytoexplorer-devel:v2.0.0 .

3. Check image has been built successfully: docker image ls

Start Docker container & mount local drives

1. Either pull down pre-built image from Docker Hub (docker pull dhammill/cytoexplorer-devel:v2.0.0) or build image locally as above.

2. Run the CytoExploreR version 2.0.0 docker image inside a container and mount directory (edit /path/to/mount). Remove dhammill below if image was built locally.

docker run --rm -dit --mount type=bind,source=/path/to/mount,destination=/home/rstudio/project -p 8787:8787 -e PASSWORD=cytoexplorer dhammill/cytoexplorer-devel:v2.0.0

3. Open localhost:8787 in a web browser.

4. Log into the RStudio session using username = rstudio and password = cytoexplorer.