You'll need a 64-bit operating system, internet access, and Python 2.7.x OR Python 3.3 or greater.
If you are running khmer in a HPC environment or for other reasons do not have root access try creating a virtual environment as described in the OS X instructions below (even if you are on linux) and then installing khmer in that newly created virtual environment.
From a terminal download the virtualenv package and create a virtual environment with it:
curl -O https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz
tar xzf virtualenv*
cd virtualenv-*; python2.7 virtualenv.py ../khmerEnv; cd ..
source khmerEnv/bin/activate
Go to Installing khmer inside the virtualenv to install khmer itself.
Install the python development environment, virtualenv, pip, gcc, and g++.
On recent Debian and Ubuntu this can be done with:
sudo apt-get install python2.7-dev python-virtualenv python-pip gcc \
g++
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/writable/directory/
python2.7 -m virtualenv khmerEnv
source khmerEnv/bin/activate
Linux users without root access can try the OS X instructions above.
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 khmer's command-line interface.
When returning to khmer after installing it you will need to reactivate the virtualenv first:
source khmerEnv/bin/activate