granek/singularity-rstudio-tidyverse

Deprecated

This image is deprecated.
It has been superseded by granek/singularity-rstudio-base.

Singularity RStudio Server with Tidyverse and Knitting

Singularity image for [RStudio Server with tidyverse and knitting support]. It was built on top of the Singularity image nickjer/singularity-rstudio

This README was shamelessly modified from [https://github.com/nickjer/singularity-rstudio] This is still a work in progress.

Build

You can build a local Singularity image named singularity-rstudio-tidyverse.simg with:

sudo singularity build singularity-rstudio-tidyverse.simg Singularity

Deploy

Instead of building it yourself you can download the pre-built image from Singularity Hub with:

singularity pull --name singularity-rstudio-tidyverse.simg shub://granek/singularity-rstudio-tidyverse

Run

RStudio Server

The rserver command is launched using the default run command:

singularity run singularity-rstudio-tidyverse.simg

or as an explicit app:

singularity run --app rserver singularity-rstudio-tidyverse.simg

Example:

$ singularity run --app rserver singularity-rstudio-tidyverse.simg --help
command-line options:

verify:
  --verify-installation arg (=0)        verify the current installation

server:
  --server-working-dir arg (=/)         program working directory
  --server-user arg (=rstudio-server)   program user
  --server-daemonize arg (=0)           run program as daemon
  --server-app-armor-enabled arg (=1)   is app armor enabled for this session
  --server-set-umask arg (=1)           set the umask to 022 on startup

...

Simple Password Authentication

To secure the RStudio Server you will need to:

1. Launch the container with the environment variable RSTUDIO_PASSWORD set to a password of your choosing.
2. Launch the rserver command with the PAM helper script rstudio_auth.

An example is given as:

RSTUDIO_PASSWORD="password" singularity run singularity-rstudio-tidyverse.simg \
  --auth-none 0 \
  --auth-pam-helper rstudio_auth

Now when you attempt to access the RStudio Server you will be presented with a log in form. You can log in with your current user name and password you set in RSTUDIO_PASSWORD.

LDAP Authentication

Another option is using an LDAP (or Active Directory) server for authentication. Configuration of the LDAP authentication script ldap_auth is handled through the following environment variables:

• LDAP_HOST - the host name of the LDAP server
• LDAP_USER_DN - the formatted string (where %s is replaced with the username supplied during log in) of the bind DN used for LDAP authentication
• LDAP_CERT_FILE - the file containing the CA certificates used by the LDAP server (default: use system CA certificates)

An example for an LDAP server with signed SSL certificate from a trusted CA:

export LDAP_HOST=ldap.example.com
export LDAP_USER_DN='cn=%s,dc=example,dc=com'
singularity run singularity-rstudio-tidyverse.simg \
  --auth-none 0 \
  --auth-pam-helper-path ldap_auth

An example for an LDAP server with a self-signed SSL certificate:

export LDAP_HOST=ldap.example.com
export LDAP_USER_DN='cn=%s,dc=example,dc=com'
export LDAP_CERT_FILE=/ca-certs.pem
singularity run \
  --bind /path/to/ca-certs.pem:/ca-certs.pem \
  singularity-rstudio-tidyverse.simg \
    --auth-none 0 \
    --auth-pam-helper-path ldap_auth

Note that we had to bind mount the CA certificates file from the host machine into the container and specify the container's path in LDAP_CERT_FILE (not the host's path).

R and Rscript

See nickjer/singularity-r for more information on how to run R and Rscript from within this Singularity image.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/granek/singularity-rstudio-tidyverse.

License

The code is available as open source under the terms of the MIT License.