Hi,
I made some fixes to the code (ldd issues, env vars..etc) of the shell script "convertFromXSQ.sh".
convertFromXSQ.sh shell script try to find $XSQ_TOOLS environment variable first, if $XSQ_TOOLS is defined then set rootDir variable.
Ubuntu Linux 11.04 (Natty) (glibc 2.13)
Step 1. Converting XSQ to CSFASTA/QUAL
(clic screenshots)

Step 2. Results
