Installing and running khmer¶
You'll need a 64-bit operating system, internet access, and Python 2.7.x OR Python 3.3 or greater.
Build requirements¶
OS X¶
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
Linux¶
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.
Installing khmer inside the virtualenv¶
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
Run the tests¶
After installing you can run the embedded test suite. If you are running an OSX system you should also add !linux to prevent linux-specific tests from failing.:
nosetests khmer --attr '!known_failing,!huge'
If the nosetests binary isn't installed then:
pip2 install khmer[tests]
nosetests khmer --attr '!known_failing,!huge'