.. vim: set filetype=rst
============================
Installing and running khmer
============================
You'll need Python 2.7+ and internet access.
The khmer project currently works with Python 2.6 but we target Python 2.7+.
Build requirements
------------------
OS X
^^^^
If you just want to use the khmer project tools and not develop them then
skip to step 4.
#) Install Xcode from the `Mac App Store (requires root)
`_.
#) `Register as an Apple Developer `__.
#) Install the Xcode command-line tools: Xcode -> preferences ->
Downloads -> Command Line Tools (requires root).
#) From a terminal download the virtualenv package and create a
virtual environment with it. You'll need the URL of the `latest
virtualenv release
`__. ::
curl -O https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.x.y.tar.gz
tar xzf virtualenv*
cd virtualenv-*; python2.7 virtualenv.py ../khmerEnv; cd ..
source khmerEnv/bin/activate
Linux
^^^^^
#) Install the python development environment, virtualenv, pip, and gcc.
- On recent Debian and Ubuntu this can be done with::
sudo apt-get install python2.7-dev python-virtualenv python-pip gcc
- For RHEL6::
sudo yum install -y python-devel python-pip git gcc gcc-c++ make
sudo pip install virtualenv
#) Create a virtualenv and activate it::
cd a/writeable/directory/
python2.7 -m virtualenv khmerEnv
source khmerEnv/bin/activate
Linux users without root access can try step 4 from the OS X instructions above.
Latest stable release
---------------------
#) Use pip to download, build, and install khmer and its dependencies::
pip2 install khmer
#) The scripts are now in the ``env/bin`` directory and ready for your
use. You can directly use them by name, see :doc:`scripts`.
#) When returning to khmer after installing it you will need to
reactivate the virtualenv first::
source khmerEnv/bin/activate
Latest development branch
-------------------------
Repeat the above but modify the pip install line::
pip2 install git+https://github.com/ged-lab/khmer.git@master#egg=khmer
You can change ``master`` in the above command to the name of another branch.
Run the tests
^^^^^^^^^^^^^
If you're running a version of ``pip`` less than 1.4 and you want to run the
tests then you should upgrade ``pip``::
pip2 install --user --upgrade pip
Repeat the appropriate installation procedure from above but add "--no-clean"
to the ``pip`` invocation.
The source will be in the ``khmerEnv/build/khmer`` directory. Run
``make test`` there.