requires.txt

# latest setutools required for automatic cythonization
setuptools>=1.1
pyparsing>=1.5.7
cython>=0.19
numpy>=1.7
# not available in py3, use mysql-client instead
# MySQL-python>1.2.3
PyYAML>=3.1.0
alignlib-lite>=0.2.3
biopython>=1.61
drmaa>=0.5
matplotlib-venn>=0.5
matplotlib>=1.3.0
# used in pipeline_exome
beautifulsoup4>=4.5.3
networkx>=1.8.1
openpyxl>=1.5.7
pandas>=0.12.0
pysam>=0.8.4
rdflib>=0.4.1
psycopg2>=2.5
rpy2>=2.6

# for pipeline_Geneset
httplib2>=0.10.3
intermine>=1.09
toposort>=1.5
mygene>=3.0.0

# note: does not install as a requirement, but directly via pip is ok
# pyBigWig>=0.3.3

ruffus>=2.4
scipy>=0.11
#https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2
#-e hg+http://bitbucket.org/james_taylor/bx-python#egg=bx-python-0.7.2
sphinx>=1.0.5
sphinxcontrib-programoutput>=0.8
sqlalchemy>=0.7.0
weblogo>=3.0
# not in py3
ggplot>=0.11.5
xlwt>=0.7.4
pybedtools>=0.6.5
pep8>=1.4.0
CGATReport>=0.7.5