Updates to example analysis in README

[ressy]

This proposes a few updates to the README to match the latest iGUIDE behavior I saw when running through the example analysis.

• Without specifying a config file path for iguide setup I get setup: error: the following arguments are required: CONFIG_FILE but it works as written in the example (so I took out the bit about not needing the configuration file argument)
• The rule compress_unique_sites implicitly removes the plaintext version, so I updated the filename in the README to match and switched to zcat instead of cat.
• The iguide eval command gives me an error (""invalid input found on input connection") and I saw that the help text says a conf file path should be given first. I updated the example command to give the simulation config file instead of the original RDS file. (But double-check me on this one!)

If this is right it might need updating in readthedocs too. Everything else ran smoothly all the way through to HTML and PDF report files. Thanks Chris!

[cnobles]

Thanks a ton for going through this Jesse. I'm working on another update (v0.9.9) and should be ready to merge it shortly. I went through your comments and changes and agree with most of them (others I had changed some behavior in the current update). I added your changes to my most recent commit in the README.txt and the docs pages (commit e438131828cf82b176926fc0cc587f5260e8a1d4).