[khmer] khmer

[C. Titus Brown]

On Mon, Jul 29, 2013 at 01:00:29PM +0000, Scott McElroy wrote:
> Titus,
> 
> Is there a manual for khmer?  Specifically I am looking for a list of options that can be used.  Even more specifically, is there an output option and how is it implemented.  -output, -o, or >> and do I specify a file name or just a path ?

Hi Scott,

please take a look here!

http://khmer.readthedocs.org/en/latest/

and ask questions!  Probably the most useful page for you is here:

http://khmer.readthedocs.org/en/latest/scripts.html

Note that all of the scripts under scripts/ will take '-h' as an option,
to print out command line help.

To answer what I think is your primary question -- currently khmer relies
almost entirely on default output file names.  So, for example,
normalize-by-median.py will append '.keep' to each file as it is processed.
We're thinking about how to make this more flexible.

cheers,
--titus
-- 
C. Titus Brown, ctb at msu.edu