R – Mathematica in batch mode from the command line on Mac OS X

Bash Space-Separated (e.g., --option argument)

cat >/tmp/demo-space-separated.sh <<'EOF'
#!/bin/bash

POSITIONAL=()
while [[ $# -gt 0 ]]; do
  key="$1"

  case $key in
    -e|--extension)
      EXTENSION="$2"
      shift # past argument
      shift # past value
      ;;
    -s|--searchpath)
      SEARCHPATH="$2"
      shift # past argument
      shift # past value
      ;;
    -l|--lib)
      LIBPATH="$2"
      shift # past argument
      shift # past value
      ;;
    --default)
      DEFAULT=YES
      shift # past argument
      ;;
    *)    # unknown option
      POSITIONAL+=("$1") # save it in an array for later
      shift # past argument
      ;;
  esac
done

set -- "${POSITIONAL[@]}" # restore positional parameters

echo "FILE EXTENSION  = ${EXTENSION}"
echo "SEARCH PATH     = ${SEARCHPATH}"
echo "LIBRARY PATH    = ${LIBPATH}"
echo "DEFAULT         = ${DEFAULT}"
echo "Number files in SEARCH PATH with EXTENSION:" $(ls -1 "${SEARCHPATH}"/*."${EXTENSION}" | wc -l)
if [[ -n $1 ]]; then
    echo "Last line of file specified as non-opt/last argument:"
    tail -1 "$1"
fi
EOF

chmod +x /tmp/demo-space-separated.sh

/tmp/demo-space-separated.sh -e conf -s /etc -l /usr/lib /etc/hosts

Output from copy-pasting the block above

FILE EXTENSION  = conf
SEARCH PATH     = /etc
LIBRARY PATH    = /usr/lib
DEFAULT         =
Number files in SEARCH PATH with EXTENSION: 14
Last line of file specified as non-opt/last argument:
#93.184.216.34    example.com

Usage

demo-space-separated.sh -e conf -s /etc -l /usr/lib /etc/hosts

Bash Equals-Separated (e.g., --option=argument)

cat >/tmp/demo-equals-separated.sh <<'EOF'
#!/bin/bash

for i in "$@"; do
  case $i in
    -e=*|--extension=*)
      EXTENSION="${i#*=}"
      shift # past argument=value
      ;;
    -s=*|--searchpath=*)
      SEARCHPATH="${i#*=}"
      shift # past argument=value
      ;;
    -l=*|--lib=*)
      LIBPATH="${i#*=}"
      shift # past argument=value
      ;;
    --default)
      DEFAULT=YES
      shift # past argument with no value
      ;;
    *)
      # unknown option
      ;;
  esac
done
echo "FILE EXTENSION  = ${EXTENSION}"
echo "SEARCH PATH     = ${SEARCHPATH}"
echo "LIBRARY PATH    = ${LIBPATH}"
echo "DEFAULT         = ${DEFAULT}"
echo "Number files in SEARCH PATH with EXTENSION:" $(ls -1 "${SEARCHPATH}"/*."${EXTENSION}" | wc -l)
if [[ -n $1 ]]; then
    echo "Last line of file specified as non-opt/last argument:"
    tail -1 $1
fi
EOF

chmod +x /tmp/demo-equals-separated.sh

/tmp/demo-equals-separated.sh -e=conf -s=/etc -l=/usr/lib /etc/hosts

Output from copy-pasting the block above

FILE EXTENSION  = conf
SEARCH PATH     = /etc
LIBRARY PATH    = /usr/lib
DEFAULT         =
Number files in SEARCH PATH with EXTENSION: 14
Last line of file specified as non-opt/last argument:
#93.184.216.34    example.com

Usage

demo-equals-separated.sh -e=conf -s=/etc -l=/usr/lib /etc/hosts

To better understand ${i#*=} search for "Substring Removal" in this guide. It is functionally equivalent to `sed 's/[^=]*=//' <<< "$i"` which calls a needless subprocess or `echo "$i" | sed 's/[^=]*=//'` which calls two needless subprocesses.

Using bash with getopt[s]

getopt(1) limitations (older, relatively-recent getopt versions):

• can't handle arguments that are empty strings
• can't handle arguments with embedded whitespace

More recent getopt versions don't have these limitations. For more information, see these docs.

POSIX getopts

Additionally, the POSIX shell and others offer getopts which doen't have these limitations. I've included a simplistic getopts example.

cat >/tmp/demo-getopts.sh <<'EOF'
#!/bin/sh

# A POSIX variable
OPTIND=1         # Reset in case getopts has been used previously in the shell.

# Initialize our own variables:
output_file=""
verbose=0

while getopts "h?vf:" opt; do
  case "$opt" in
    h|\?)
      show_help
      exit 0
      ;;
    v)  verbose=1
      ;;
    f)  output_file=$OPTARG
      ;;
  esac
done

shift $((OPTIND-1))

[ "${1:-}" = "--" ] && shift

echo "verbose=$verbose, output_file='$output_file', Leftovers: $@"
EOF

chmod +x /tmp/demo-getopts.sh

/tmp/demo-getopts.sh -vf /etc/hosts foo bar

Output from copy-pasting the block above

verbose=1, output_file='/etc/hosts', Leftovers: foo bar

Usage

demo-getopts.sh -vf /etc/hosts foo bar

The advantages of getopts are:

1. It's more portable, and will work in other shells like dash.
2. It can handle multiple single options like -vf filename in the typical Unix way, automatically.

The disadvantage of getopts is that it can only handle short options (-h, not --help) without additional code.

There is a getopts tutorial which explains what all of the syntax and variables mean. In bash, there is also help getopts, which might be informative.

Windows Server 2003 and later (i.e. anything after Windows XP 32 bit) provide the where.exe program which does some of what which does, though it matches all types of files, not just executable commands. (It does not match built-in shell commands like cd.) It will even accept wildcards, so where nt* finds all files in your %PATH% and current directory whose names start with nt.

Try where /? for help.

Note that Windows PowerShell defines where as an alias for the Where-Object cmdlet, so if you want where.exe, you need to type the full name instead of omitting the .exe extension.