bioruby: 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/bioruby - from package: ruby-bio

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

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