
Instructions for RosettaCon 2010 protocol capture

Take off your headphones and visualize the following:
you can send this archive back in time to yourself before you
knew squat about rosetta ... make this as clear and self contained
as you can, because pre-you doesn't know every trick or
dependency in your code. (p.s. pre-you can also see the SVN
dir you make)

This protocol is meant for not-you, and not-you also
won't like hard links in scripts to files or paths that are
only on you-you's computer.

1) rename the directory "Template" to your protocol name, no spaces 

2) fill out the file "README with the indicated information 

   *** include svn location and revision number of your code **
  
   *** if the code you used is not checked into trunk,       **
   *** upload your code to an svn workspace                  ** 
   ***  SEE how to create and work with the SVN workspaces:
   ***   https://wiki.rosettacommons.org/index.php/Tools:Subversion#Workspaces
 

3) put a command line in the file "run_example"

4) put input ond output files for the "run_example" command in the respective directories   

5) add any relavent scripts and instructions to "scripts" directory, please minimally comment 
   scripts with emphasis on how to run, connect and otherwise operate these scripts
    
6) upload to folder on SVN server ( will be, initially under trunk ## name from doug ## )   

  trac: https://svn.rosettacommons.org/trac/browser/trunk/RosettaCon2010/protocol_capture

  For people to check in they would want to use the commands bellow...

  $ svn checkout -N
     https://svn.rosettacommons.org/source/trunk/RosettaCon2010/protocol_capture/
  $ cd protocol_capture
  $ cp -r /path/to/my/new_protocol .
  $ svn add new_protocol
  $ svn commit -m "Committing my awesome new protocol that I am going to
     talk about at RosettaCon2010 so that all my bask in its purifying
     light"
 

Note: There is a command line flag
that will have the options system print all of the accessed options
during a run. This will not give you all of the options that could be
used by the protocol, only a list of what was accessed in that run.
That could however serve as a very good starting point of the
"Important Flags" section of the README.
--out::show_accessed_options

Note: It might be nice to compare these to full-length integration
test with more documentation about the work flow, as I suspect anyone
that will do the protocol capture has probably written a unit test. 

Credits: thanks to Glenn Butterfoss, Doug Renfrew for building this template and Xavier Ambroggio for early discussions about the 
capture, release and breeding of wild protocols.
