Quartus Programmer Command Linux

1). login as root:

[mul@localhost]$ su

2). turn off selinux temporarily:

[root@localhost mul]# /usr/sbin/setenforce 0
[root@localhost mul]# chmod 777 -R /opt/altera9.1/

3) logout as root or using the other console :

[mul@localhost]$ quartus_pgm --cable="USB-Blaster [USB 3-1.3]" --mode=JTAG -o p\;name.sof

Semicolon under shells such as bash is a command separator. You should escape the semicolon with \