slurmjobs

slurmjobs provides helper functions for interacting with SLURM-managed high-performance-computing environments from R. It includes functions for creating submittable jobs (including array jobs), monitoring partitions, and extracting info about running or complete jobs. For details, check out the documentation site.

It was developed at JHPCE with SLURM 22.05.9 in mind, but is intended to generalize to other clusters and newer SLURM versions.

Installation instructions

Get the latest stable R release from CRAN. Then install slurmjobs from GitHub with:

remotes::install_github("LieberInstitute/slurmjobs")

Citation

Below is the citation output from using citation('slurmjobs') in R. Please run this yourself to check for any updates on how to cite slurmjobs.

print(citation("slurmjobs"), bibtex = TRUE)
#> To cite package 'slurmjobs' in publications use:
#> 
#>   LieberInstitute (2024). _slurmjobs: Helper Functions for SLURM Jobs_.
#>   doi:10.18129/B9.bioc.slurmjobs
#>   <https://doi.org/10.18129/B9.bioc.slurmjobs>,
#>   https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package
#>   version 1.1.0, <http://www.bioconductor.org/packages/slurmjobs>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {slurmjobs: Helper Functions for SLURM Jobs},
#>     author = {{LieberInstitute}},
#>     year = {2024},
#>     url = {http://www.bioconductor.org/packages/slurmjobs},
#>     note = {https://github.com/LieberInstitute/slurmjobs/slurmjobs - R package version 1.1.0},
#>     doi = {10.18129/B9.bioc.slurmjobs},
#>   }
#> 
#>   LieberInstitute (2024). "slurmjobs: Helper Functions for SLURM Jobs."
#>   _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
#>   <https://www.biorxiv.org/content/10.1101/TODO>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {slurmjobs: Helper Functions for SLURM Jobs},
#>     author = {{LieberInstitute}},
#>     year = {2024},
#>     journal = {bioRxiv},
#>     doi = {10.1101/TODO},
#>     url = {https://www.biorxiv.org/content/10.1101/TODO},
#>   }

Please note that the slurmjobs was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the slurmjobs project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.