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
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.
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