bowtie2-build: 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 Debian possible default full paths are:

/usr/bin/bowtie2-build - from package: bowtie2

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

Error in other languages:
bowtie2-build: bevel nie gevind nie
bowtie2-build: comandă negăsită
bowtie2-build: comando não encontrado
bowtie2-build: commande introuvable
bowtie2-build: command not found
bowtie2-build: käsku ei ole
bowtie2-build: không tìm thấy lệnh
bowtie2-build: komanda nerasta
bowtie2-build: Kommando nicht gefunden.
bowtie2-build: kommandot finns inte
bowtie2-build: komut yok
bowtie2-build: nie znaleziono polecenia
bowtie2-build: níor aimsíodh an t-ordú
bowtie2-build: no se encontró la orden
bowtie2-build: no s'ha trobat l'ordre
bowtie2-build: opdracht niet gevonden
bowtie2-build: parancs nem található
bowtie2-build: perintah tidak ditemukan
bowtie2-build: príkaz nenájdený
bowtie2-build: příkaz nenalezen
bowtie2-build: команда не найдена
bowtie2-build: командата не е открита
bowtie2-build: 命令找不到
bowtie2-build: コマンドが見つかりません