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https://github.com/nickjer/singularity-rstudio
RStudio Server in a Singularity container
https://github.com/nickjer/singularity-rstudio
rstudio-server singularity-image
Last synced: 5 days ago
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RStudio Server in a Singularity container
- Host: GitHub
- URL: https://github.com/nickjer/singularity-rstudio
- Owner: nickjer
- License: mit
- Created: 2018-01-18T14:38:53.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2024-07-17T08:30:13.000Z (6 months ago)
- Last Synced: 2024-12-24T18:12:01.636Z (12 days ago)
- Topics: rstudio-server, singularity-image
- Language: Python
- Homepage: https://singularity-hub.org/collections/463
- Size: 22.5 KB
- Stars: 54
- Watchers: 6
- Forks: 41
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Singularity RStudio Server
[](https://travis-ci.org/nickjer/singularity-rstudio)
[](https://singularity-hub.org/collections/463)
[](https://opensource.org/licenses/MIT)
Singularity image for [RStudio Server]. It was built on top of the base
Singularity image [nickjer/singularity-r].
This is still a work in progress.
## Build
You can build a local Singularity image named `singularity-rstudio.simg` with:
```sh
sudo singularity build singularity-rstudio.simg Singularity
```
## Deploy
Instead of building it yourself you can download the pre-built image from
[Singularity Hub](https://www.singularity-hub.org) with:
```sh
singularity pull --name singularity-rstudio.simg shub://nickjer/singularity-rstudio
```
## Run
### RStudio Server
The `rserver` command is launched using the default run command:
```sh
singularity run singularity-rstudio.simg
```
or as an explicit app:
```sh
singularity run --app rserver singularity-rstudio.simg
```
Example:
```console
$ singularity run --app rserver singularity-rstudio.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:
```sh
RSTUDIO_PASSWORD="password" singularity run singularity-rstudio.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:
```sh
export LDAP_HOST=ldap.example.com
export LDAP_USER_DN='cn=%s,dc=example,dc=com'
singularity run singularity-rstudio.simg \
--auth-none 0 \
--auth-pam-helper-path ldap_auth
```
An example for an LDAP server with a self-signed SSL certificate:
```sh
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.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/nickjer/singularity-rstudio.
## License
The code is available as open source under the terms of the [MIT License].
[RStudio Server]: https://www.rstudio.com/products/rstudio/
[nickjer/singularity-r]: https://github.com/nickjer/singularity-r
[MIT License]: http://opensource.org/licenses/MIT