The project was implemented in Python v.2.7.7. The following packages are required to run most of the code that makes up this project:

  • Scikit-learn
  • Numpy
  • Scipy

To be careful though, it is worthwhile to print a full list of the packages installed on the computer this code was run on.


In [1]:
import sys
print sys.version


2.7.7 (default, Jun  3 2014, 01:46:20) 
[GCC 4.9.0 20140521 (prerelease)]

In [1]:
!pip freeze


Cython==0.20.1
GnuPGInterface==0.3.2
Jinja2==2.7.3
Landscape-Client==14.01
Mako==0.9.1
MarkupSafe==0.23
MySQL-python==1.2.3
PAM==0.4.2
Pillow==2.3.0
Pmw==1.3.2
PyNAST==1.2
SQLAlchemy==0.8.4
SecretStorage==2.0.0
Twisted-Core==13.2.0
apt-xapian-index==0.45
argparse==1.2.1
backports.ssl-match-hostname==3.4.0.2
beautifulsoup4==4.2.1
biom-format==1.1.2
biopython==1.63
chardet==2.0.1
cogent==1.5.3
colorama==0.2.5
configobj==4.7.2
cutadapt==1.3
cvxopt==1.1.4
decorator==3.4.0
gdata==2.0.18
html5lib==0.999
httplib2==0.8
iotop==0.6
ipython==2.1.0
ipython-cytoscape.js==0.1.0.dev1
joblib==0.7.1
keyring==3.5
khmer==1.0
launchpadlib==1.10.2
lazr.restfulclient==0.13.3
lazr.uri==1.0.3
lxml==3.3.3
matplotlib==1.3.1
mpi4py==1.3.1
networkx==1.9
nose==1.3.1
numexpr==2.2.2
numpy==1.8.1
oauth==1.0.1
openpyxl==1.7.0
pandas==0.14.1
patsy==0.2.1
pexpect==3.1
pyOpenSSL==0.13
pycrypto==2.6.1
pycurl==7.19.3
pygobject==3.12.0
pymol==1.7.0.0
pyparsing==2.0.1
pysam==0.7.7
pyserial==2.6
pysqlite==2.6.3
python-apt==0.9.3.5
python-dateutil==2.2
python-debian==0.1.21-nmu2ubuntu2
pytz==2014.4
pyzmq==14.3.1
qcli==0.1.0
reportlab==3.0
requests==2.2.1
rpy==1.0.3
scikit-learn==0.15.0
scipy==0.14.0
screed==0.7.1
simplegeneric==0.8.1
simplejson==3.3.1
six==1.7.3
ssh-import-id==3.21
statsmodels==0.5.0
tables==3.1.1
tornado==3.2.2
urllib3==1.7.1
virtualenv==1.11.4
wadllib==1.3.2
wsgiref==0.1.2
xlrd==0.9.2
xlwt==0.7.5
zope.interface==4.0.5