QuartusforLinux

Quartus        = /opt/altera9.1sp1/quartus
IP Megacore = /opt/altera9.1sp1/ip
Nios II EDS   = /opt/altera9.1sp1/nios2eds
Modelsim      = /opt/altera9.1sp1/modelsim

(Ed., we don't need "9.1sp1" numbered for each subdir when the parent dir already spelled it. while "nios2eds" and "ip" are more officially used by Altera.)

SERVER localhost <your nic> 1800
VENDOR alterad "/opt/altera9.1sp1/quartus/linux/alterad"
VENDOR mgcld "/opt/altera9.1sp1/modelsim/modeltech/linuxaloem/mgls/lib/mgcld"

# USB-Blaster
BUS=="usb", SYSFS{idVendor}=="09fb", SYSFS{idProduct}=="6001",MODE="0666", PROGRAM="/bin/sh -c 'K=%k; K=$${K#usbdev}; printf /proc/bus/usb/%%03i/%%03i $${K%%%%.*} $${K#*.}'", RUN+="/bin/chmod 0666 %c"

Setup NIOS Shell

Find out your system perl path. This is because the Altera perl lib didn't have all the modules reuqired to process PTF file.
eg, 
/usr/lib/perl5/5.10.0 on Fedora10,
/usr/lib/perl5/5.8.8 on Centos5.

Login as a user. Put these lines in a script file , say "n2sdk", in ~/bin dir. remember "chmod +x n2sdk".

#!/bin/bash
# Run this for a Nios II SDK bash shell
export LM_LICENSE_FILE=1800@localhost
SOPC_KIT_NIOS2=/opt/altera9.1sp1/nios2eds
export SOPC_KIT_NIOS2
SOPC_BUILDER_PATH_91=/opt/altera9.1sp1/nios2eds
export SOPC_BUILDER_PATH_91
unset GCC_EXEC_PREFIX
QUARTUS_ROOTDIR=/opt/altera9.1sp1/quartus
export QUARTUS_ROOTDIR
export PERL5LIB=/usr/lib/perl5/5.8.8
bash --rcfile $QUARTUS_ROOTDIR/sopc_builder/bin/nios_bash

Run Software

Open a shell terminal, enter "n2sdk". This will open a Bourne-again shell (bash) with a pre-configured environment.

------------------------------------------------
Welcome To Altera SOPC Builder

Version 9.1sp1, Built Tue Oct 28 11:01:00 PDT 2008
------------------------------------------------

------------------------------------------------
Welcome to the Nios II Embedded Design Suite
Version 9.1sp1, Built Tue Oct 28 11:27:40 PDT 2008

Example designs can be found in
    /opt/altera9.1sp1/nios2eds/examples

------------------------------------------------
(You may add a startup script: /opt/altera9.1sp1/nios2eds/user.bashrc)
~
[NiosII EDS]$

Now you can run quartus, just enter "quartus" in this command shell.
[NiosII EDS]$ quartus

If quartus ask you the license file for the first run, enter "1800@localhost" .

You can find more usage of command line tools on section 2-4 of  Embedded Design Handbook (highly recommended reading).

Now, you can install nios2gcc tools and uClinux-dist. Build the uClinux kernel image.

Then plug in your USB Blaster, connect to your dev board (2C35 here).
You can try out the jtag port.

[NiosII EDS]$ jtagconfig
1) USB-Blaster [USB 5-1.2]
  020B40DD   EP2C35
[NiosII EDS]$ nios2-configure-sof
/opt/altera9.1sp1/nios2eds/examples/verilog/niosII_cycloneII_2c35/full_featured/
NiosII_cycloneII_2c35_full_featured.sof
Info: *******************************************************************
Info: Running Quartus II Programmer
Info:
Command: quartus_pgm --no_banner --mode=jtag -o
p;/opt/altera8.0/nios2eds/examples/verilog/niosII_cycloneII_2c35/full_featured/
NiosII_cycloneII_2c35_full_featured.sof
Info: Using programming cable "USB-Blaster [USB 5-1.2]"
Info: Started Programmer operation at Fri Dec  8 11:35:01 2006
Info: Configuring device index 1
Info: Device 1 contains JTAG ID code 0x020B40DD
Info: Configuration succeeded -- 1 device(s) configured
Info: Successfully performed operation(s)
Info: Ended Programmer operation at Fri Dec  8 11:35:04 2006
Info: Quartus II Programmer was successful. 0 errors, 0 warnings
    Info: Processing ended: Fri Dec  8 11:35:04 2006
    Info: Elapsed time: 00:00:22
[NiosII EDS$ nios2-download -g ~/uClinux-dist/images/zImage
Using cable "USB-Blaster [USB 5-1.2]", device 1, instance 0x00
Pausing target processor: OK
Initializing CPU cache (if present)
OK
Downloaded 1016KB in 16.2s (62.7KB/s)
Verified OK
Starting processor at address 0x04500000
[NiosII EDS$ nios2-terminal
nios2-terminal: connected to hardware target using JTAG UART on cable
nios2-terminal: "USB-Blaster [USB 5-1.2]", device 1, instance 0
nios2-terminal: (Use the IDE stop button or Ctrl-C to terminate)
Uncompressing Linux... Ok, booting the kernel.
Linux version 2.6.Uncompressing Linux... Ok, booting the kernel.
Linux version 2.6.17-uc1 (hippo@darkstar) (gcc version 3.4.6) #46 
PREEMPT Thu Dec 7 15:22:06 CST 2006

You can try out flash programmer, or add flash file conversion to your build script. Or run GDB debugger.
Happy hacking.

Miscellaneous Fixes

1. If the Nios II EDS installer does not work, edit the install script at line 143 :
        From : x=${x/~/$HOME}
        To     : ##x=${x/~/$HOME}
   
   
2. If the modelsim installer doesnt work, edit the install.ms script :
   At line 172 :
       From    : tar xfo {$script_path}/modeltech_altera_unix.tar
       To        : tar xfo {$script_path}/modeltech_altera_unix.tar --no-same-permissions
   At line 174 :
       From    : tar xfo {$script_path}/modeltech_altera_unix.tar $file1.Z $file2.Z $file3.Z
       To        : tar xfo {$script_path}/modeltech_altera_unix.tar $file1.Z $file2.Z $file3.Z --no-same-permissions
   
   
3. If the SOPC builder keeps giving language error (minor problem). This is an issue with Perl. To fix it, type this in a terminal :
          cd /usr/lib/locale
          cp -r en_US.utf8 en_US
   
   
4. To fix the “Unknown Linux Processor” issue, download the file 'arch' and put it in /bin. You will need administrator access to do this.
   
   
5. Sometimes the Licences in Quartus menu will not open. This can be solved by copying the provided file 'libX11.so.6.2' into/opt/altera7.2/quartus/linux. You will need administrator privileges. Then type this in a terminal:
        cd /opt/altera7.2/quartus/linux
        sudo ln -s libX11.so.6.2 libX11.so.6

Old Info (Outdated)

To Install Quartus 8.1 look here:  Quartus8forLinux

The version of Linux distro is important. Some latest distro use udev, and need extra hacking, see Instalation on unsupported distributions. Though it is possible to use other Linux disto or version, it might be difficult for newbies.

To install Altera Design Software 7.2 in Ubuntu Linux, follow this step by step tutorial : Altera Software Installation Tutorial for Ubuntu.pdf
This tutorial show how to install all the tools including setting up usbfs for USB blaster. It might also apply for other Linux distros based on Debian.