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:
To be careful though, it is worthwhile to print a full list of the packages installed on the computer this code was run on.
import sys
print sys.version
2.7.7 (default, Jun 3 2014, 01:46:20) [GCC 4.9.0 20140521 (prerelease)]
!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