biopython>=1.61
boto>=2.34.0
Cython>=0.19
ipyparallel>=4.0.0
ipython-cluster-helper>=0.4.9
Logbook>=0.6.0
lxml>=3.3.5
msgpack-python>=0.4.0
nose>=1.3.0
pandas>=0.14.1
progressbar>=2.3.0
pybedtools>=0.6.8
pysam>=0.8.2.1
pyzmq>=2.2.0
PyYAML>=3.10
toolz>=0.7.1
tornado>=3.1.0
# soft dependencies -- not required for bcbio-nextgen-vm
azure>=0.11.1
arrow>=0.4.4
awscli>=1.7.14
bioblend>=0.4.3
bcbreport>=0.99.14
click>=3.3
cnvkit>=0.3.4
cutadapt==1.8.3
fadapa>=0.3.1
fabric>=1.7.0
gffutils>=0.8.4rc1
joblib>=0.8.4
openpyxl>=1.6.1,<2.0.0
path.py>=7.0
psutil>=1.2.0
pythonpy>=0.3.6
python-dateutil>=2.1
PyVCF>=0.6.7
sh>=1.07
tabulate>=0.7.3
scikit-learn>=0.15.2
seaborn>=0.5.0
bcbio-nextgen==0.9.3

biopython>=1.61
boto>=2.34.0
Cython>=0.19
ipyparallel>=4.0.0
ipython-cluster-helper>=0.4.9
Logbook>=0.6.0
lxml>=3.3.5
msgpack-python>=0.4.0
nose>=1.3.0
pandas>=0.14.1
progressbar>=2.3.0
pybedtools>=0.6.8
pysam>=0.8.2.1
pyzmq>=2.2.0
PyYAML>=3.10
toolz>=0.7.1
tornado>=3.1.0
# soft dependencies -- not required for bcbio-nextgen-vm
azure>=0.11.1
arrow>=0.4.4
awscli>=1.7.14
bioblend>=0.4.3
bcbreport>=0.99.14
click>=3.3
fadapa>=0.3.1
fabric>=1.7.0
gffutils>=0.8.4rc1
joblib>=0.8.4
openpyxl>=1.6.1,<2.0.0
path.py>=7.0
psutil>=1.2.0
python-dateutil>=2.1
PyVCF>=0.6.7
sh>=1.07
tabulate>=0.7.3
scikit-learn>=0.15.2
seaborn>=0.5.0
bcbio-nextgen==0.9.3

Move external python-based packages to --tools
Move external python-based packages to --tools

Packages we don't import in bcbio and call only via the command line are
now installed via --tools using the standard conda packaging approach.
This avoids needing to keep dependencies up to date in the requirements.
