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This was referenced Dec 12, 2024
eitsupi
requested changes
Dec 13, 2024
| ## Importing a Rocker Image | ||
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| Use the `singularity pull` command to import the desired Rocker image from Docker Hub into a (compressed, read-only) Singularity Image File: | ||
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| ```bash | ||
| singularity pull docker://rocker/rstudio:4.2 | ||
| singularity pull docker://rocker/rstudio:4.4.2 |
| /usr/lib/rstudio-server/bin/rserver --www-address=127.0.0.1 | ||
| --scratch /run,/var/lib/rstudio-server \ | ||
| --workdir $(mktemp -d) \ | ||
| rstudio_4.4.2.sif \ |
| rstudio_4.2.sif \ | ||
| /usr/lib/rstudio-server/bin/rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user=$(whoami) | ||
| --scratch /run,/var/lib/rstudio-server \ | ||
| rstudio_4.4.2.sif \ |
| # personal libraries from any R installation in the host environment | ||
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| R_LIBS_USER=${HOME}/R/rocker-rstudio/4.4.2 |
| singularity exec --cleanenv \ | ||
| --scratch /run,/tmp,/var/lib/rstudio-server \ | ||
| --workdir ${workdir} \ | ||
| rstudio_4.4.2.sif \ |
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| :::{.callout-note} | ||
| In this guide, *Singularity* can refer to either [SingularityCE](https://sylabs.io/singularity/) or [Apptainer](https://apptainer.org/). | ||
| While Apptainer is generally [compatible with Singularity commands and environment variables](https://apptainer.org/docs/user/latest/singularity_compatibility.html), Apptainer users may wish to replace the `singularity` command with `apptainer`, and `SINGULARITY` with `APPTAINER` in environment variables. | ||
| ::: |
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| :::{.callout-note} | |
| In this guide, *Singularity* can refer to either [SingularityCE](https://sylabs.io/singularity/) or [Apptainer](https://apptainer.org/). | |
| While Apptainer is generally [compatible with Singularity commands and environment variables](https://apptainer.org/docs/user/latest/singularity_compatibility.html), Apptainer users may wish to replace the `singularity` command with `apptainer`, and `SINGULARITY` with `APPTAINER` in environment variables. | |
| ::: | |
| :::{.callout-note} | |
| In this guide, *Singularity* can refer to either [SingularityCE](https://sylabs.io/singularity/) or [Apptainer](https://apptainer.org/). | |
| While Apptainer is generally [compatible with Singularity commands and environment variables](https://apptainer.org/docs/user/latest/singularity_compatibility.html), Apptainer users may wish to replace the `singularity` command with `apptainer`, and `SINGULARITY` with `APPTAINER` in environment variables. | |
| ::: |
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Updates the Singularity guide:
rserver --server-userin job script (singularity on HPC with slurm rocker-versioned2#837)(Specify .Rprofile and .Renviron when using singularity rocker-versioned2#855)
python3instead ofpython(the latter may be python 2 or absent on some hosts)--scratchand--workdir(though shouldn't make a difference with a single-node allocation)