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https://github.com/nickjer/singularity-r
R in a Singularity container
https://github.com/nickjer/singularity-r
r singularity-image
Last synced: about 2 months ago
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R in a Singularity container
- Host: GitHub
- URL: https://github.com/nickjer/singularity-r
- Owner: nickjer
- License: mit
- Created: 2018-01-18T13:54:16.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2022-09-16T11:41:35.000Z (over 2 years ago)
- Last Synced: 2023-08-01T05:12:22.731Z (over 1 year ago)
- Topics: r, singularity-image
- Homepage: https://cloud.sylabs.io/library/nickjer/default/singularity-r
- Size: 17.6 KB
- Stars: 26
- Watchers: 3
- Forks: 31
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Singularity R
[](https://github.com/nickjer/singularity-r/actions)
[](https://opensource.org/licenses/MIT)
Singularity image for [R].
This is still a work in progress.
## Build
You can build a local Singularity image named `singularity-r.sif` with:
```sh
sudo singularity build singularity-r.sif singularity-r.def
```
## Deploy
Instead of building it yourself you can download the pre-built image from the
[Cloud Library](https://cloud.sylabs.io/library) with:
```sh
singularity pull singularity-r.sif library://nickjer/default/singularity-r:4.2.1
```
> **WARNING:** This pre-built image comes with OpenBLAS installed using the
> Debian binary packages. Be sure to run any tests with libraries that leverage
> OpenBLAS in your enviroment. If you notice any odd results it may be best to
> build this image from scratch on the machine you intend to run it on. See
> instructions under the Build section above.
>
> Or alternatively you can mount the locally installed OpenBLAS library into
> the container using...
>
> ```sh
> singularity run \
> --bind "/path/on/host/to/libopenblas.so:/usr/lib/R/lib/libblas.so.3" \
> singularity-r.sif
> ```
## Run
### R
The `R` command is launched using the default run command:
```sh
singularity run singularity-r.sif
```
or as an explicit app:
```sh
singularity run --app R singularity-r.sif
```
Example:
```console
$ singularity run --app R singularity-r.sif --version
...
```
### Rscript
The `Rscript` command is launched as an explicit app:
```sh
singularity run --app Rscript singularity-r.sif
```
Example:
```console
$ singularity run --app Rscript singularity-r.sif --version
...
```
## Contributing
Bug reports and pull requests are welcome on GitHub at
https://github.com/nickjer/singularity-r.
## License
The code is available as open source under the terms of the [MIT License].
[R]: https://www.r-project.org/
[MIT License]: http://opensource.org/licenses/MIT