shuffleBed: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On CentOS possible default full paths are:

/usr/bin/shuffleBed - from package: BEDTools

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/shuffleBed - from package: BEDTools

You may install the required package with command apt-get install {package}

Error in other languages:
shuffleBed: bevel nie gevind nie
shuffleBed: comandă negăsită
shuffleBed: comando não encontrado
shuffleBed: commande introuvable
shuffleBed: command not found
shuffleBed: käsku ei ole
shuffleBed: không tìm thấy lệnh
shuffleBed: komanda nerasta
shuffleBed: Kommando nicht gefunden.
shuffleBed: kommandot finns inte
shuffleBed: komut yok
shuffleBed: nie znaleziono polecenia
shuffleBed: níor aimsíodh an t-ordú
shuffleBed: no se encontró la orden
shuffleBed: no s'ha trobat l'ordre
shuffleBed: opdracht niet gevonden
shuffleBed: parancs nem található
shuffleBed: perintah tidak ditemukan
shuffleBed: príkaz nenájdený
shuffleBed: příkaz nenalezen
shuffleBed: команда не найдена
shuffleBed: командата не е открита
shuffleBed: 命令找不到
shuffleBed: コマンドが見つかりません