An escaping of the variable within bash script

Question

My bash script writes an another bash script using printf.

printf \"#!/bin/bash
HOME=${server}
file=gromacs*
file_name=\\$(basename \"\\${file}\")
date=\\$(date          


        

Answer 1

Use a quoted heredoc.

{
  ## print the header, and substitute our own value for HOME
  printf '#!/bin/bash\nHOME=%q\n' "$server"
  ## EVERYTHING BELOW HERE UNTIL THE EOF IS LITERAL
  cat <<'EOF'
file=( gromacs* )
(( ${#file[@]} == 1 )) && [[ -e $file ]] || {
  echo "ERROR: Exactly one file starting with 'gromacs' should exist" >&2
  exit 1
}
file_name=$(basename "${file}")
date=$(date +"%m_%d_%Y")

for sim in "$HOME"/* ; do
 if [[ -d $sim ]]; then
  simulation=$(basename "$sim")
  (cd "${sim}" && exec cp "$file" "${server}/${results}/${file_name}.${simulation}.${date}")
  echo "${file_name} from ${simulation} has been collected!"
 fi
done
EOF
} >"${output}/collecter.sh"

---

Note:

• Inside a quoted heredoc (cat <<'EOF'), no substitutions are performed, so no escaping is needed. We're thus able to write our code exactly as we want it to exist in the generated file.
• When generating code, use printf %q to escape values in such a way as to evaluate back to their original values. Otherwise, a variable containing $(rm -rf ~) could cause the given command to be run (if it were substituted inside literal single quotes, making the contents $(rm -rf ~)'$(rm -rf ~)' would escape them).
• Glob expansions return a list of results; the proper data type in which to store their results is an array, not a string. Thus, file=( gromacs* ) makes the storage of the result in an array explicit, and the following code checks for both the case where we have more than one result, and the case where our result is the original glob expression (meaning no matches existed).
• All expansions need to be quoted to prevent string-splitting. This means "$HOME"/*, not $HOME/* -- otherwise you'll have problems whenever a user has a home directory containing whitespace (and yes, this does happen -- consider Windows-derived platforms where you have /Users/Firstname Lastname, or sites where you've mounted a volume for home directories off same).
• pushd and popd are an interactive extension, as opposed to a tool intended for writing scripts. Since spawning an external program (such as cp) involves a fork() operation, and any directory change inside a subshell terminates when that subshell does, you can avoid any need for them by spawning a subshell, cd'ing within that subshell, and then using the exec builtin to replace the subshell's PID with that of cp, thus preventing the fork that would otherwise have taken place to allow cp to be started in a separate process from the shell acting as its parent.