The transrate package has been modified to work with Salmon v0.8.2. 

(This is the most recent binary available for Max OSX. The Linux
Binaries are 0.13.1).

1. The old bin directory has been replaced by a new bin with
 bam-read and snap-aligner (which appear to be stand-alone binaries)
 and symbolic links to the salmon 0.8.2 binary and its associated 
 library files.

2. lib/app/lib/transrate/salmon.rb has been modified to remove 
   deprecated command options that cause errors if used with 
   the current version of salmon. salmon_quant_alignment.help
   in that directory is the output of the salmon quant --help-alignment
   command. 
3. lib/app/deps/deps.yaml has been modified to change the salmon version
   to 0.8.2
