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Installing and running khmer
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You'll need git, Python and `virtualenv
<http://pypi.python.org/pypi/virtualenv>`__.

Note: The python development environment needs to be installed, too; on
Debian, this can be done with:

  apt-get install python-dev

On OS X, you'll need XCode installed, I believe.

Then, check out screed and khmer::

  git clone git://github.com/ctb/screed.git
  git clone git://github.com/ctb/khmer.git

Create and activae a virtualenv working environment::

 python -m virtualenv env
 . env/bin/activate

Install 'screed' (note, the argument to 'easy_install' here is the directory
containing screed)::

 easy_install screed

Build khmer::

 cd khmer
 make clean all

Run the tests::

 easy_install nose
 make test

To run khmer scripts, you will need to either install the Python
package by running::

 easy_install /path/to/khmer

OR by setting the PYTHONPATH::

 export PYTHONPATH=/path/to/khmer/python

The scripts are all located in khmer/scripts.