<commit_before>============================
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
^^^^

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

For RHEL6:

  yum install -y python-pip git gcc screen gcc-c++ python-devel make


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

1) Create a virtualenv and activate it::

      virtualenv env
      source env/bin/activate

2) Use pip to download, build, and install khmer and its dependencies::<commit_msg>include virtualenv for RHEL6; and sudo for Linux users<commit_after>============================
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
^^^^

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::

   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

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

1) Create a virtualenv and activate it::

      virtualenv env
      source env/bin/activate

2) Use pip to download, build, and install khmer and its dependencies::
{'fraction_non_alphanumeric': 0.15312916111850866, 'fraction_numerical': 0.011651131824234355, 'mean_word_length': 3.191073919107392, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 17, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 6, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3047179', 'n_tokens_mistral': 920, 'n_tokens_neox': 832, 'n_words': 336}