Shell Scripting

Shell Scripting Expert

Expert guidance for writing robust, maintainable Bash and Zsh scripts with best practices for automation and command-line tool usage.

Script Structure Essentials

Start every script with:

#!/usr/bin/env bash
set -euo pipefail
IFS=$'\n\t'

• set -e: Exit on error
• set -u: Error on undefined variables
• set -o pipefail: Catch errors in pipes
• IFS=$'\n\t': Safer word splitting

Critical Best Practices

1. Always quote variables: "$variable" not $variable
2. Use [[ for conditionals (Bash): if [[ "$var" == "value" ]]; then
3. Check command existence: if command -v git &> /dev/null; then
4. Avoid parsing ls: Use globs or find instead
5. Use arrays for lists: files=("file1" "file2") not space-separated strings
6. Handle errors with traps:

   trap cleanup EXIT
   trap 'echo "Error on line $LINENO"' ERR
   

Common Patterns

Argument Parsing

while [[ $# -gt 0 ]]; do
    case $1 in
        -h|--help) usage; exit 0 ;;
        -v|--verbose) VERBOSE=true; shift ;;
        -*) echo "Unknown option: $1"; exit 1 ;;
        *) break ;;
    esac
done

Safe File Iteration

# Prefer this (handles spaces, newlines correctly):
while IFS= read -r -d '' file; do
    echo "Processing: $file"
done < <(find . -type f -name "*.txt" -print0)

# Or with simple globs:
for file in *.txt; do
    [[ -e "$file" ]] || continue  # Skip if no matches
    echo "Processing: $file"
done

User Confirmation

read -rp "Continue? [y/N] " response
if [[ "$response" =~ ^[Yy]$ ]]; then
    echo "Continuing..."
fi

Colored Output

RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m'  # No Color

echo -e "${GREEN}Success${NC}"
echo -e "${RED}Error${NC}" >&2

Modern Tool Alternatives

When appropriate, suggest these modern replacements:

• ripgrep (rg) → faster than grep
• fd → faster than find
• fzf → interactive filtering
• jq → JSON processing
• yq → YAML processing
• bat → cat with syntax highlighting
• eza → enhanced ls

Function Organization

usage() {
    cat <<EOF
Usage: ${0##*/} [OPTIONS] <args>
Description of what this script does.
OPTIONS:
    -h, --help      Show this help
    -v, --verbose   Verbose output
EOF
}

main() {
    # Main logic here
    :
}

Snakemake & Shells

• Snakemake uses Bash: By default, Snakemake executes shell: directives using /bin/bash -euo pipefail.
• Write Bash, not Fish: Even if your terminal is Fish, write rule commands in standard Bash syntax.
• Strict Mode: Snakemake enables strict mode automatically.

Zsh-Specific Features

When user specifies Zsh:

• Advanced globbing: **/*.txt (recursive), *.txt~*test* (exclude pattern)
• Parameter expansion: ${var:u} (uppercase), ${var:l} (lowercase)
• Associative arrays: typeset -A hash; hash[key]=value
• Extended globbing: Enable with setopt extended_glob

Security Considerations

• Never eval untrusted input
• Validate user input before use
• Use mktemp for temporary files: TEMP_FILE=$(mktemp)
• Be explicit with rm -rf operations
• Check for TOCTOU (Time-Of-Check-Time-Of-Use) race conditions
• Don't store secrets in scripts; use environment variables or secret managers

Performance Tips

• Use built-ins over external commands ([[ ]] vs test, $(( )) vs expr)
• Avoid unnecessary subshells: var=$(cat file) → var=$(<file)
• Use read not cat | while: while read -r line; do ... done < file
• Consider xargs -P or GNU parallel for parallel processing

Quick Reference Template

See references/template.sh for a complete, production-ready script template with all best practices incorporated.