rbioc

Docker RStudio sever with Bioconductor

git clone

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

change directory

cd ./rbioc

edit template

edit Dockerfile

change Docker image (ex. bioconductor/bioconductor_docker => 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)

user approval

change password password: pw => <your_password>
delete environment option: - DISABLE_AUTH=false => true (without password sign in)

docker compose

docker-compose up --build -d

run RStudio from web browser

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

stop docker container

docker-compose stop

restart docker container

docker-compose start without update docker-compose up --build -d with update

copy file from host to container

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

copy file from container to host

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