https://github.com/mooerslab/bashfunctions4oscer

Bash functions to ease work on supercomputer using SLURM
https://github.com/mooerslab/bashfunctions4oscer

automate-boring-tasks bash-scripting data-science data-wrangling directory-trees file-renaming file-wrangling git oscer python remote remote-computers remote-server slurm ssh supercomputing

Last synced: 10 days ago
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Bash functions to ease work on supercomputer using SLURM

• Host: GitHub
• URL: https://github.com/mooerslab/bashfunctions4oscer
• Owner: MooersLab
• License: mit
• Created: 2022-10-12T15:59:57.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-05-27T12:22:45.000Z (about 1 year ago)
• Last Synced: 2025-06-13T06:08:02.578Z (10 days ago)
• Topics: automate-boring-tasks, bash-scripting, data-science, data-wrangling, directory-trees, file-renaming, file-wrangling, git, oscer, python, remote, remote-computers, remote-server, slurm, ssh, supercomputing
• Language: Shell
• Homepage:
• Size: 41 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# Bash functions to ease work on the University of Oklahoma's Supercomputer 

The University of Oklahoma's supercomputer is called *Schooner* and is run by the Oklahoma Center for Supercomputing Education and Research [(OSCER)](https://www.ou.edu/oscer).

The supercomputer uses the [SLURM](https://slurm.schedmd.com/overview.html) job queuing software. 

Some of the functions ease the use of this system.

Other functions ease doing boring tasks.

These functions can be adapted to run on local unix-like machines (e.g.,  macOS and Linux)!

The file paths will need editing.

The bash script calls two Python scripts in the subfolder.

May this script inspire you to write new bash functions!

## Usage in bash or zsh shells

These functions work in either bash or zsh shells.

Source the .bashFunctions file from your .bashrc or .zshrc file.

Then, enter the function name in the terminal and hit return or enter to get a printout in the terminal of the documentation, which includes examples. 

## Useful functions of note

- The *gac* function combines `git add` and `git commit -m`.

- The *take* function combines `mkdir` and `cd` to the new directory.

- The *rmspaces* function removes those annoying whitespaces in the filenames of all files in the current directory.

- The *rmunderscores* function removes underscores in the filenames of all files in the current directory.

- The *rmcommas* function removes commas in the filenames of all files in the current directory.

## Table of function names and descriptions (planned)

## Related repositories

- [emacs4oscer](https://github.com/MooersLab/emacs4oscer)

- [vimrc4oscer](https://github.com/MooersLab/vimrc4oscer)

## Sources of funding

- NIH: R01 CA242845

- NIH: R01 AI088011

- NIH: P30 CA225520 (PI: R. Mannel)

- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)