requirements.txt

argparse==1.4.0
toil-msk[cwl]==3.21.1
codecov==2.0.15

nose==1.3.7
coloredlogs==5.2
coverage==4.3.4
avro==1.8.1
backports.functools-lru-cache==1.5
backports.ssl-match-hostname==3.5.0.1
bd2k-python-lib==1.14a1.dev48
CacheControl==0.11.7
certifi==2019.3.9
chardet==3.0.4
cycler==0.10.0
dill==0.2.7.1
docker==2.5.1
docker-pycreds==0.3.0
docutils==0.14
funcsigs==1.0.2
future==0.17.0
futures==3.2.0
galaxy-lib==17.9.3
idna==2.6
ipaddress==1.0.22
isodate==0.6.0
joblib==0.13.2
junit-xml==1.8
kiwisolver==1.0.1
lockfile==0.12.2
matplotlib==2.2.2
numpy==1.16.1
pandas==0.20.0
pybedtools==0.7.10
PyPDF2==1.26.0
pysam==0.15.2
ruamel.yaml==0.14.0
scikit-learn==0.19.1
scipy==1.1.0
seaborn==0.9.0
xlrd==1.1.0

# ACCESS-Variants
filemagic==1.6.0
pyvcf==0.6.8
openpyxl==1.8.6
# todo: need to upgrade iAnnotateSV to 0.24.0
# pandas==0.16.2
coloredlogs==5.2
pillow==3.4.2
biopython==1.65
reportlab==3.3.0