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)

2. Register as an Apple Developer

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
   source 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 khmer’s command-line interface.

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

   source 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
make test

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