USB-Blaster under Linux?

The routines which perform the sysid checks, on the host (Win32/Linux), are pretty much the same. All Run/Download/Debug traffic is routed through nios2-gdb-server.

What are the differences between what your PTF contains, in the sysid peripheral, and what the IDE is reporting? Posting your exact error message could help.

Also, if I were you, I would try doing the following on your Linux box:

1. Generating/Re-generating your SOPC Builder system.

2. Building your project in the IDE.

3. Compiling in Quartus II.

In my experience, IDE Builds and SOPC Builder generations are noticeably quicker running in Linux.

Good luck!

- slacker