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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# slurmjobs
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[](https://github.com/LieberInstitute/slurmjobs/issues)
[](https://github.com/LieberInstitute/slurmjobs/pulls)
[](https://github.com/LieberInstitute/slurmjobs/actions/workflows/check-bioc.yml)
[](https://app.codecov.io/gh/LieberInstitute/slurmjobs?branch=devel)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
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`slurmjobs` provides helper functions for interacting with [SLURM](https://slurm.schedmd.com/)-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](http://research.libd.org/slurmjobs/).
It was developed at [JHPCE](https://jhpce.jhu.edu/) 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](http://cran.r-project.org/). Then install `slurmjobs` from [GitHub](https://github.com/LieberInstitute/slurmjobs) with:
```{r 'install_gh', eval = FALSE}
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__.
```{r 'citation', eval = requireNamespace('slurmjobs')}
print(citation("slurmjobs"), bibtex = TRUE)
```
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](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://LieberInstitute.github.io/slurmjobs) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.