============================
Installing and running khmer
============================

You'll need Python 2.7+ and internet access. 

Build requirements
------------------

OS X
^^^^

1) Install Xcode from the `Mac App Store (requires root)
   <https://developer.apple.com/xcode/>`_

2) `Register as an Apple Developer <https://developer.apple.com/register>`_

3) Install the Xcode command-line tools: Xcode -> preferences ->
   Downloads -> Command Line Tools (requires root)

4) From a terminal install virtualenv/pip::

      curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
      python get-pip.py --user
      #add the python user binaries to your path if needed
      echo "PATH=\$PATH:`python2.7 -c "import site; print site.getuserbase()"`/bin; export PATH" >> ~/.bash_profile
      source ~/.bash_profile
      pip install --user virtualenv


Linux
^^^^^

Install the python development environment, virtualenv, pip, and
gcc; on Debian and Ubuntu this can be done with::

   apt-get install python2.7-dev python-virtualenv python-pip gcc

Latest stable release
---------------------

1) Create a virtualenv and activate it::

      virtualenv env
      . env/bin/activate

2) Use pip to download, build, and install khmer and its dependencies::

      pip install khmer

3) The scripts are now in the ``env/bin`` directory and ready for your
   use. You can directly use them by name, see :doc:`scripts`.

4) When returning to khmer after installing it you will need to
   reactivate the virtualenv first::

      . env/bin/activate

Latest development branch
-------------------------

Repeat the above but modify the pip install line::

   pip install -e git+git@github.com:ged-lab/khmer.git@master#egg=khmer

Run the tests
^^^^^^^^^^^^^

From within your activated virtualenv you will find the source in
env/src/khmer::

   cd env/src/khmer
   python setup.py nosetests