biopython>=1.61
boto>=2.34.0
Cython>=0.19
ipython>=2.0.0
ipython-cluster-helper>=0.3.3
Logbook>=0.6.0
lxml>=3.3.5
msgpack-python>=0.4.0
nose>=1.3.0
pysam>=0.8.0
pyzmq>=2.2.0
PyYAML>=3.10
toolz>=0.6.0
tornado>=3.1.0
#temporary dependency to work around issue with pandas and 1.3.1
google-api-python-client>=0.1.2,<1.3.1
# soft dependencies -- not required for bcbio-nextgen-vm
arrow>=0.4.4
arvados-python-client>=0.1.1405019228.4a7ca04
bioblend>=0.4.3
chanjo>=2.0.2
click>=3.3
cnvkit>=0.2.5
cutadapt==1.4.2
fabric>=1.7.0
gffutils>=0.8.2
HTSeq >= 0.5.4p5
joblib>=0.7.0d
openpyxl>=1.6.1,<2.0.0
path.py>=7.0
prettyplotlib>=0.1.7
psutil>=1.2.0
pybedtools>=0.6.8
pythonpy>=0.3.6
PyVCF>=0.6.7
sh>=1.07
# To be added after 0.8.4 release
# scikit-learn>=0.15.2
bcbio-nextgen==0.8.3
