sgejobs

This package contains helper functions for Son of Grid Engine (SGE) cluster jobs, mostly with usage at the Joint High Performance Computing Exchange (JHPCE) cluster in mind. Please check the package documentation website for more information about how to use sgejobs.

Installation instructions

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

BiocManager::install("LieberInstitute/sgejobs")

Citation

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

print(citation("sgejobs"), bibtex = TRUE)
#> To cite package 'sgejobs' in publications use:
#> 
#>   Collado-Torres L (2023). _sgejobs: Helper functions for SGE jobs at
#>   JHPCE_. R package version 0.99.2,
#>   <https://github.com/LieberInstitute/sgejobs>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {sgejobs: Helper functions for SGE jobs at JHPCE},
#>     author = {Leonardo Collado-Torres},
#>     year = {2023},
#>     note = {R package version 0.99.2},
#>     url = {https://github.com/LieberInstitute/sgejobs},
#>   }

Please note that the sgejobs 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 sgejobs 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.