README

This repo contains personal configurations for configs (git, tmux, R), variables and functions.

Appends to the existing .bashrc.

Layout

dotfiles/
├── bin/
│   └── checksum_verify.sh     # Slurm batch script (md5 verification)
├── shell/
│   ├── bashrc.sh              # entry point, sourced from the system ~/.bashrc
│   ├── exports.sh             # portable environment variables
│   ├── functions.sh           # custom shell functions
│   ├── aliases.sh             # shell aliases (git, R, Slurm)
│   └── prompt.sh              # git-aware cross-shell prompt
├── nvim/                      # symlinked to ~/.config/nvim
│   ├── init.lua               # entry: settings, lazy.nvim bootstrap
│   └── lua/config/
│       ├── plugins.lua        # colorscheme, Treesitter, Nextflow syntax
│       ├── filetypes.lua      # .nf / nextflow.config detection
│       └── keymaps.lua        # paste-mode toggle
├── dotfiles.local.template    # template for machine-local settings (tracked)
├── install.sh                 # bootstrap: symlinks + appends source block
├── tmux.conf                  # symlinked to ~/.tmux.conf
├── Rprofile                   # symlinked to ~/.Rprofile
├── .gitignore
└── README.md

Install

folder="dotfiles"

git clone git@github.com:andreyhgl/dotfiles.git "$folder" &&
	cd "$folder" &&
	bash install.sh

# edit the machine-local config
vi ~/.dotfiles.local
source ~/.bashrc

install.sh is idempotent — safe to run again after a git pull.

Functions

Defined in shell/functions.sh.

checksum_verify

Submit a checksum verification job (the function wraps sbatch -A "$ACCOUNT"):

checksum_verify path/to/checksums.md5

Results appear in the directory the job ran in:

• _CHECKSUM.OK — all checksums matched
• _CHECKSUM.FAILED — one or more failed (contains md5sum's output)

Can also be called directly:

sbatch -A <account> ~/.local/bin/checksum_verify.sh path/to/checksums.md5

Interactive Slurm session

salloc is wrapped (in shell/functions.sh) to apply sensible defaults and print a summary before launching the session. Arguments are positional and optional:

salloc [time] [mem_GB] [cpus]

Argument	Default	Example
time	3:00:00	6:00:00
mem_GB (G appended automatically)	20 → 20G	40 → 40G
cpus	1	4

salloc                 # 3:00:00, 20G, 1 cpu
salloc 6:00:00 40 4    # 6h, 40G, 4 cpus

Requires ACCOUNT to be set (in ~/.dotfiles.local). To bypass the wrapper and call the real binary directly, use command salloc ....

Aliases & shortcuts

Defined in shell/aliases.sh.

git

Command	Expands to	Notes
gs	git status --short	Compact status
ga	git add
gd	git diff	Unstaged changes
gds	git diff --staged	Staged changes
gc	git commit -m "$*"	Function — no quotes needed: gc fix the bug. Quote if using special chars (> \ ').
gca	git commit --amend	Amend, edit message
gcan	git commit --amend --no-edit	Amend, keep message
gsw	git switch	Switch branches
gp	git push
gpl	git pull
gl	git log --graph ...	Pretty one-line graph log
gt	git for-each-ref ... refs/tags	Tags, newest first, with date/tagger/subject
gb	git branch -a ...	All branches, newest commit first, with subject + relative date

R

Command	Expands to	Notes
R	R --no-save --no-restore	Stateless interactive R; Ctrl-D quits without the save prompt. Interactive only — pass flags explicitly in batch jobs.

Slurm

Command	Expands to	Notes
jobinfo	squeue -u $USER	Your jobs
jobinfo_full	squeue -u $USER -o "..." | column -t | less -FRXS	Wide, scrollable job table

Neovim

Config lives in nvim/ and is symlinked to ~/.config/nvim by install.sh. Provides syntax highlighting for bash, R, and Nextflow, plus the nightfly colorscheme.

Requirements

• Neovim 0.9+ (uses vim.filetype.add and modern Lua APIs).
• A true-color terminal — nightfly is true-color only. On macOS use iTerm2, kitty, WezTerm, or Ghostty (Terminal.app does not do full 24-bit color). termguicolors is already enabled in init.lua.
• A C compiler for Treesitter parser compilation. On macOS: xcode-select --install.

First launch

1. Open nvim. lazy.nvim bootstraps itself and installs the plugins automatically (you'll see the install UI).
2. Treesitter compiles the bash/r/groovy parsers. If it doesn't run automatically, run :TSUpdate.
3. Restart nvim. On HPC, run the first launch on a login node (which has network access) so plugins and parsers download; compute nodes are often offline.

Notes

• Treesitter is pinned to its master branch — the newer main branch is an incompatible rewrite with a different API.
• If highlighting looks wrong or plugins seem stuck, reset the cache: rm -rf ~/.local/share/nvim/lazy/nvim-treesitter then reopen nvim.

Prompt

Defined in shell/prompts.sh.

Show git states in prompt, works in zsh and bash.

[user@machine ~] (main) $ 

Configs

Tmux

Switch panes using Ctrl+hjkl (vim-style) without prefix

Machine-local config

Per-cluster values (like ACCOUNT) live in ~/.dotfiles.local, which is not tracked in git. Copy the template and edit it on each machine:

cp dotfiles.local.template ~/.dotfiles.local

Uninstall

Remove the marked block from ~/.bashrc:

# >>> dotfiles >>>
...
# <<< dotfiles <<<

or restore the backup install.sh made:

cp ~/.bashrc.backup ~/.bashrc

Then remove the symlink: rm ~/.local/bin/checksum_verify.sh