bedtools: 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/bedtools - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/bedtools - from package: BEDTools

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

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