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Shell - Basic Setup

Essential shell configuration for a productive Unix environment.

Quick setup of script folders in correct path

Make sure you create these 2 folders, ~/.local/bin is where many installers but their scripts and ~/bin is the folder you should use for your scripts and wrappers. 

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mkdir -p ~/bin ~/.local/bin

then add this line at the end of your shell config file (.bashrc for Linux or .zshrc for Mac).

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[ -d "$HOME/bin" ] && export PATH="$HOME/bin:"$HOME/.local/bin:$PATH"

everything below is optional

File Creation Permissions

Set umask

Control file creation permissions to ensure security:

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# Set umask to 0007
# This makes new files group-writable but not world-readable
umask 0007

What this does: - 0007 sets permissions to u=rwx, g=rwx, o=--- - Files created are 660 (rw-rw----) - Directories created are 770 (rwxrwx----) - Group members can read/write, others cannot access - Balances security with team collaboration

Add this early in your shell profile (.bashrc for Linux or .zshrc for Mac).

PATH Configuration

Organize Your PATH

Properly structure your PATH for predictable binary resolution:

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# User-local binaries (takes precedence)
export PATH="$HOME/.local/bin:$PATH"

# Traditional user bin directory
export PATH="$PATH:$HOME/bin"

# Cargo binaries (Rust)
export PATH="$PATH:$HOME/.cargo/bin"

Order matters: - ~/.local/bin first - User-installed tools take precedence - System PATH in middle - Standard locations - ~/bin last - Legacy user directory - ~/.cargo/bin last - Rust binaries

Set Micromamba as Default Conda

If using micromamba for environment management:

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# Set micromamba as default conda
export CONDA_EXE="$(command -v micromamba)"
export MAMBA_EXE="${CONDA_EXE}"

Rootless Container Configuration

Podman/Docker Support

For rootless Podman or Docker:

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# Set runtime directory for rootless containers
export XDG_RUNTIME_DIR="/run/user/$(id -u)"

# Alias docker to podman if available
if command -v podman &> /dev/null; then
    alias docker='podman'
fi

Why this matters: - Allows running containers without root privileges - XDG_RUNTIME_DIR provides runtime file storage - docker=podman alias simplifies workflow if migrating from Docker

Shell Profile Setup

Bash Configuration

Interactive Shell Config - Edit ~/.bashrc:

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# File creation permissions
umask 0007

# PATH Configuration
export PATH="$HOME/.local/bin:$PATH"
export PATH="$PATH:$HOME/bin"
export PATH="$PATH:$HOME/.cargo/bin"

# Set default editor
export EDITOR=vim
export GIT_EDITOR=vim

# Language
export LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8

# Conda/Micromamba
export CONDA_EXE="$(command -v micromamba)"

# Rootless container support
export XDG_RUNTIME_DIR="/run/user/$(id -u)"

# Container aliases
if command -v podman &> /dev/null; then
    alias docker='podman'
fi

# Add useful aliases
alias ll='ls -lah'
alias cd..='cd ..'
alias clear-cache='rm -rf ~/.cache'

Login Shell Config - Edit ~/.profile or ~/.bash_profile:

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# Source .bashrc for interactive login shells
if [ -n "$BASH_VERSION" ]; then
    if [ -f "$HOME/.bashrc" ]; then
        . "$HOME/.bashrc"
    fi
fi

# SSH Keychain - ONLY in login shell (skip in Slurm PTY)
if [[ -z "$SLURM_PTY_PORT" ]]; then
    eval $(~/.local/bin/keychain --quiet --eval id_ed25519)
fi

Zsh Configuration

Interactive Shell Config - Edit ~/.zshrc:

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# File creation permissions
umask 0007

# PATH Configuration
export PATH="$HOME/.local/bin:$PATH"
export PATH="$PATH:$HOME/bin"
export PATH="$PATH:$HOME/.cargo/bin"

# Set default editor
export EDITOR=vim
export GIT_EDITOR=vim

# Language
export LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8

# Conda/Micromamba
export CONDA_EXE="$(command -v micromamba)"

# Rootless container support
export XDG_RUNTIME_DIR="/run/user/$(id -u)"

# Container aliases
if command -v podman &> /dev/null; then
    alias docker='podman'
fi

# Add useful aliases
alias ll='ls -lah'
alias cd..='cd ..'

Login Shell Config - Edit ~/.zprofile:

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# SSH Keychain - ONLY in login shell (skip in Slurm PTY)
if [[ -z "$SLURM_PTY_PORT" ]]; then
    eval $(~/.local/bin/keychain --quiet --eval id_ed25519)
fi

Essential Environment Variables

Set these in your shell configuration:

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# Editor (for Git, system tools)
export EDITOR=vim
export GIT_EDITOR=vim

# Language and encoding
export LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8

# File creation permissions
umask 0007

# Container support
export XDG_RUNTIME_DIR="/run/user/$(id -u)"

Color Schemes

Directory Colors for Better Visibility

Add to your shell configuration for improved readability:

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# Export LS_COLORS with improved directory visibility
# Change directory color from dark blue (01;34) to cyan (01;36)
export LS_COLORS="di=01;36:ln=01;36:so=01;31:pi=40;33:ex=01;32:bd=40;33;01:cd=40;33;01:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzop=01;31:*.xz=01;31:*.zst=01;31:*.zstd=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:"

Key color changes: - di=01;36 - Directories in cyan (easier to see than dark blue) - ln=01;36 - Symlinks in cyan - ex=01;32 - Executables in green

Vim Color Scheme

Configure Vim for better visibility in ~/.vimrc:

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" Enable syntax highlighting
syntax on

" Use desert color scheme
colorscheme desert

Command History

Keep your shell history clean and effective:

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# Increase history size
export HISTSIZE=10000
export HISTFILESIZE=10000

# Ignore duplicate commands
export HISTCONTROL=ignoredups

# Ignore common commands from history
export HISTIGNORE="ls:cd:pwd:history"

SSH Keychain Auto-Loading

Smart Keychain Initialization

IMPORTANT: Add SSH keychain to your login shell profile ONLY (.profile, .bash_profile, or .zprofile), NOT to .bashrc or .zshrc:

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# SSH Keychain - Skip in Slurm computing environment
# This avoids conflicts with Slurm's PTY management
# ONLY add this to login profiles: ~/.profile, ~/.bash_profile, or ~/.zprofile
if [[ -z "$SLURM_PTY_PORT" ]]; then
    eval $(~/.local/bin/keychain --quiet --eval id_ed25519)
fi

Why login shell profile only? - Login shells (.profile, .zprofile) run once per login session - Interactive shells (.bashrc, .zshrc) run for every new shell - SSH agent should only be initialized once, not repeatedly - Prevents multiple keychain processes and agent conflicts

Why the Slurm check? - Slurm (job scheduler) has its own PTY management - Loading keychain in Slurm context can cause conflicts - Check $SLURM_PTY_PORT to detect Slurm environment - Skip keychain loading in compute jobs

Complete Configuration Example

Full ~/.bashrc (Interactive Shell Config)

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# File creation permissions
umask 0007

# PATH Configuration
export PATH="$HOME/.local/bin:$PATH"
export PATH="$PATH:$HOME/bin"
export PATH="$PATH:$HOME/.cargo/bin"

# Editor
export EDITOR=vim
export GIT_EDITOR=vim

# Language
export LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8

# Container support
export XDG_RUNTIME_DIR="/run/user/$(id -u)"

# Conda/Micromamba
export CONDA_EXE="$(command -v micromamba)"

# Directory colors (cyan for better visibility)
export LS_COLORS="di=01;36:..."

# History
export HISTSIZE=10000
export HISTFILESIZE=10000
export HISTCONTROL=ignoredups
export HISTIGNORE="ls:cd:pwd:history"

# Container aliases
if command -v podman &> /dev/null; then
    alias docker='podman'
fi

# Useful aliases
alias ..='cd ..'
alias ...='cd ../..'
alias ll='ls -lah'
alias l='ls -la'
alias cls='clear'
alias py='python'
alias serve='python -m http.server'
alias clear-cache='rm -rf ~/.cache'

Full ~/.profile (Login Shell Config)

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# Source .bashrc if it exists
if [ -n "$BASH_VERSION" ]; then
    if [ -f "$HOME/.bashrc" ]; then
        . "$HOME/.bashrc"
    fi
fi

# SSH Keychain - ONLY in login shell (skip in Slurm)
# DO NOT add this to .bashrc!
if [[ -z "$SLURM_PTY_PORT" ]]; then
    eval $(~/.local/bin/keychain --quiet --eval id_ed25519)
fi

Secure Development Environment

Your shell environment should be:

  • Secure: SSH keys with passphrases, keychain for convenience, restricted permissions (umask)
  • Clean: Well-organized PATH, proper binary resolution
  • Productive: Useful aliases, good history management, proper colors
  • Isolated: Virtual environments, container support, environment detection (Slurm)
  • Collaborative: Group-writable files (umask 0007) for team projects