Python 2.6 compatibility

Currently, salmon only works with Python 2.7+. I was able to get it working on 2.6 with only minimal changes (as not much new stuff is in use). This is helpful for running on e.g. CentOS 6, for which higher versions are not easily available.

* Specify indices in format strings, e.g. `{0}` rather than `{}` (which is only supported [in 2.7 and later](http://docs.python.org/2/library/string.html#format-string-syntax)
* Use `subprocess.Popen` instead of `subprocess.check_output` (latter [added in 2.7](http://docs.python.org/2/library/subprocess.html#subprocess.check_output))