rbioc

Docker RStudio sever with Bioconductor

git clone

git clone https://github.com/achiral/rprot.git

change directory

cd ./rprot

edit template

edit Dockerfile

change Docker image (ex. achiral/rbioc:latest => FROM docker-ID/docker-image:latest)
install R packages (see below exampe codes)
RUN install2.r pkgname1 pkgname2 RUN Rscript -e "install.packages('vector_of_package_names')" RUN Rscript -e 'BiocManager::install("vector_of_package_names")'

edit docker-compose.yml

rename Docker image (ex. image: docker-ID/docker-image:latest)
rename Docker container (ex. container_name: docker-ID/docker-container:latest)

user approval

change password (ex. pw => <your_password>)
change environment option: (- DISABLE_AUTH=true => false (activate password sign in))

docker compose

docker-compose up --build -d

run RStudio from web browser

open http://localhost:8787/(rstudio/pw (default) or <your_password>)

stop docker container

docker-compose stop (or docker-compose down)

restart docker container

docker-compose start without update (stopped docker container with docker-compose stop) docker-compose up --build -d with update (stopped docker container with docker-compose down)

copy file from host to container

docker cp <host directory> <container name>:<container ditectory> (ex. docker cp /Users/user/Dropbox/data/. rprot:/home/rstudio/rproject/data/)

copy file from container to host

docker cp <container name>:<container directory> <host directory>