updated Makefile for current version of khmer
Merge pull request #2 from ged-lab/update

Updated to deal with latest khmer version
changes for revisions
Merge branch 'master' of https://github.com/ged-lab/2012-paper-diginorm into update
updated to complete kak assembles; added gitignore
more updates for revision
make .txt into .rst
pipe notes update
pipe notes update 2
updated nb; pipeline notes
update pythonpath
Merge branch 'master' of https://github.com/ged-lab/2012-paper-diginorm
added prokka instructions and fix some bowtie