windowMaker: 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/windowMaker - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/windowMaker - from package: BEDTools
/usr/bin/windowMaker - from package: wmaker

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

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