You’ll need Python 2.7+ and internet access.
Install Xcode from the Mac App Store (requires root)
Install the Xcode command-line tools: Xcode -> preferences -> Downloads -> Command Line Tools (requires root)
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
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
Create a virtualenv and activate it:
virtualenv env
. env/bin/activate
Use pip to download, build, and install khmer and its dependencies:
pip install khmer
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.
When returning to khmer after installing it you will need to reactivate the virtualenv first:
. env/bin/activate
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For an introduction to the documentation format please see the reST primer.