Introduction

This repository contains the docker setup with all dependencies required to run the BASiCS workflow. The setup inherits from the bioconductor/bioconductor_docker.

This repository is under development - not ready to be used

Useful commands

To clone this repository

git clone https://github.com/VallejosGroup/bioconductor_docker_basics.git

To build the docker image locally (assumes you are in the correct folder)

docker build . -t bioconductor_docker_basics:0.0.1

To run the docker image via Rstudio server. The code below ensures that the files in $HOME/Documents/Github/Manuscripts/BASiCSWorkflow are available via Rstudio.

docker run -p 8787:8787 -v $HOME/Documents/Github/Manuscripts/BASiCSWorkflow:/home/rstudio/mycode -e PASSWORD=bioc bioconductor_docker_basics:0.0.1

Then access http://localhost:8787. Username: rstudio, password = bioc.

Other commands

Note: mostly copy/paste from bioconductor website

To check available images

docker image ls
docker images

To list all running containers

docker ps

To list all available containers

docker ps -a

To resume a stopped container

docker start <CONTAINER ID>

Shell into a running container

docker exec -it <CONTAINER ID> /bin/bash

Shutdown container

docker stop <CONTAINER ID>

Delete container

docker rm <CONTAINER ID>

Delete image

docker rmi bioconductor/bioconductor_docker:devel

Useful links

• Docker containers for Bioconductor
• Best practices and standards for Bioconductor Docker Images