http://seqanswers.com/forums/showthread.php?t=17514
Error :
File "./tophat", line 1003
except getopt.error, msg:
^
SyntaxError: invalid syntax
To solve :
edit tophat
#!/usr/bin/env python2
instead of
#!/usr/bin/env python
This error comes from the difference between python2 and python3.
check your path and version of python
