[Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2

[Josh Thackray]

Hi Tim,

Thanks for updating the packages! I updated using the package manager, 
however bowtie (version 1.1.1) seems to now be broken. Upon further 
investigation, it looks like only the debug binaries get installed. 
Invoking bowtie with the --debug option gives me the help message, while 
invoking bowtie with no options gives an error (No such file or directory).

Thanks,

Josh