How can I store a command in a variable in a shell script?

Use eval:

x="ls | wc"
eval "$x"
y=$(eval "$x")
echo "$y"

Do not use eval! It has a major risk of introducing arbitrary code execution.

BashFAQ-50 - I'm trying to put a command in a variable, but the complex cases always fail.

Put it in an array and expand all the words with double-quotes "${arr[@]}" to not let the IFS split the words due to Word Splitting.

cmdArgs=()
cmdArgs=('date' '+%H:%M:%S')

and see the contents of the array inside. The declare -p allows you see the contents of the array inside with each command parameter in separate indices. If one such argument contains spaces, quoting inside while adding to the array will prevent it from getting split due to Word-Splitting.

declare -p cmdArgs
declare -a cmdArgs='([0]="date" [1]="+%H:%M:%S")'

and execute the commands as

"${cmdArgs[@]}"
23:15:18

(or) altogether use a bash function to run the command,

cmd() {
   date '+%H:%M:%S'
}

and call the function as just

cmd

POSIX sh has no arrays, so the closest you can come is to build up a list of elements in the positional parameters. Here's a POSIX sh way to run a mail program

# POSIX sh
# Usage: sendto subject address [address ...]
sendto() {
    subject=$1
    shift
    first=1
    for addr; do
        if [ "$first" = 1 ]; then set --; first=0; fi
        set -- "$@" --recipient="$addr"
    done
    if [ "$first" = 1 ]; then
        echo "usage: sendto subject address [address ...]"
        return 1
    fi
    MailTool --subject="$subject" "$@"
}

Note that this approach can only handle simple commands with no redirections. It can't handle redirections, pipelines, for/while loops, if statements, etc

Another common use case is when running curl with multiple header fields and payload. You can always define args like below and invoke curl on the expanded array content

curlArgs=('-H' "keyheader: value" '-H' "2ndkeyheader: 2ndvalue")
curl "${curlArgs[@]}"

Another example,

payload='{}'
hostURL='http://google.com'
authToken='someToken'
authHeader='Authorization:Bearer "'"$authToken"'"'

now that variables are defined, use an array to store your command args

curlCMD=(-X POST "$hostURL" --data "$payload" -H "Content-Type:application/json" -H "$authHeader")

and now do a proper quoted expansion

curl "${curlCMD[@]}"

var=$(echo "asdf")
echo $var
# => asdf

Using this method, the command is immediately evaluated and its return value is stored.

stored_date=$(date)
echo $stored_date
# => Thu Jan 15 10:57:16 EST 2015
# (wait a few seconds)
echo $stored_date
# => Thu Jan 15 10:57:16 EST 2015

The same with backtick

stored_date=`date`
echo $stored_date
# => Thu Jan 15 11:02:19 EST 2015
# (wait a few seconds)
echo $stored_date
# => Thu Jan 15 11:02:19 EST 2015

Using eval in the $(...) will not make it evaluated later:

stored_date=$(eval "date")
echo $stored_date
# => Thu Jan 15 11:05:30 EST 2015
# (wait a few seconds)
echo $stored_date
# => Thu Jan 15 11:05:30 EST 2015

Using eval, it is evaluated when eval is used:

stored_date="date" # < storing the command itself
echo $(eval "$stored_date")
# => Thu Jan 15 11:07:05 EST 2015
# (wait a few seconds)
echo $(eval "$stored_date")
# => Thu Jan 15 11:07:16 EST 2015
#                     ^^ Time changed

In the above example, if you need to run a command with arguments, put them in the string you are storing:

stored_date="date -u"
# ...

For Bash scripts this is rarely relevant, but one last note. Be careful with eval. Eval only strings you control, never strings coming from an untrusted user or built from untrusted user input.

For bash, store your command like this:

command="ls | grep -c '^'"

Run your command like this:

echo $command | bash