R to be used. Assuming you are not willing to pay, this can make analyses that depend on R packages across multiple versions of R inconvenient to run.R/R Studio server pre-installed, you can easily bypass the two limitations above. A user can connect to the rocker image via an ssh tunnel, accessing R Studio server through their local web browser. Each docker image can have a unique installation of R Studio server, thus any number of R versions can be used.rocker image on a remote server.You must have docker installed on your system. To check you have docker installed, you can use:
# based on: https://www.digitalocean.com/community/questions/how-to-check-for-docker-installation
docker -v
echo $?If you don’t, install docker. A guide to installing docker on Ubuntu 18.04 can be found here.
rocker image
In order to use R Studio server, a docker image with R Studio server pre-installed is required. Bioconductor releases it’s own docker image that inherits from rocker, with other useful system dependencies for analyses of biological data pre-installed, such as core Bioconductor packages. You can download the Bioconductor docker image using:
# the 3.13 release version of Bioconductor docker image is used here
# be sure to check for an updated version as and when you use this guide
sudo docker pull bioconductor/bioconductor_docker:RELEASE_3_13To initialise a container running R Studio server on the Bioconductor docker image downloaded above, you need to execute the docker run command with various flags depending on your desired setup. rockup has a single user-level function docker_run_rserver() which is designed to make this step easier and executable within R.
First, make sure you have rockup installed. If you don’t, you can install rockup from GitHub via:
# this requires R version >= 4.0
devtools::install_github("ryten_lab/rockup")Next, run rockup::docker_run_rserver() within an R terminal on the remote server/machine where you want to use R Studio server. At a minimum, you should set the image, port and name arguments explained below. Setting the verbose argument to TRUE will print the flags that were used within the docker command and can be useful for debugging or logging.
Important: if you are running this on the Ryten lab server, it is worth making sure: 1. The port you use does not overlap with one that’s already in use. The list of in use ports can be found in the ryten_induction bookdown here. 2. If you’re occupying a new port, please add it to the list of in use ports (or ask another member to).
rockup::docker_run_rserver(
image = "bioconductor/bioconductor_docker:RELEASE_3_13", # a rocker image, or one that inherits from rocker
port = 8888, # port on which the host will have present R Studio server
name = "example", # name of docker process
verbose = TRUE # whether to print out the flags passed to the docker command
)Once the R Studio server process is running, the next step is to map the localhost port of your local machine to the port presenting R Studio server on the remote server (specified above as 8787). You can do so by executing the ssh command shown below on your local machine:
# make sure the port specified here matches the port you have used above in
# rockup::docker_run_rserver()
ssh \
-X -N -f -L localhost:8787:localhost:8787 \
user@ipIf the above ssh command has run successfully, you will now be able to access R Studio server by going to the address localhost:8787 on your local browser. The default login details for the Bioconductor docker are:
Username: rstudio
Password: bioc
More details of the Bioconductor docker can be found here.
Most analyses relies on data that is stored on the original host machine, therefore not (by default) accessible by the docker container. Therefore, it is often useful to mount the required files, allowing them to be accessible by the docker process. Mounting files can be done using rockup::docker_run_rserver() via the arguments volumes, volumes_ro.
Directories mounted using the volumes_ro argument will always have read-only access permissions on the docker container.
The user permissions for accessing files mounted using volumes argument are dictated by the USERID and GROUPID arguments. These should be set matching the user you would like to mirror the permissions of. On Linux, the USERID and GROUPID of the current user can be obtained via the bash command id. Warning: depending on the permissions, this could give your docker container the ability to delete the mounted files
Below is an example of running rockup::docker_run_rserver(), whilst mounting volumes:
# volumes - paths will be mounted with user permissions
# matching user specified by the USERID and GROUPID arguments
# volumes_ro - paths will be mounted with read-only access
rockup::docker_run_rserver(
image = "bioconductor/bioconductor_docker:RELEASE_3_13",
port = 8888,
name = "example_2",
verbose = TRUE,
volumes = c(
"/path/to/mounted/dir/that/will/match/permissions/"
),
volumes_ro = c(
"/path/to/mounted/dir/that/will/be/read_only"
),
permissions = "match",
USERID = 1000,
GROUPID = 1000
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