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GitHub / CarolinaPB / population-structural-var-calling-smoove

population structural variant calling with smoove

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CarolinaPB%2Fpopulation-structural-var-calling-smoove

Stars: 1
Forks: 3
Open Issues: 0

License: None
Language: Python
Repo Size: 1.84 MB
Dependencies: 235

Created: almost 3 years ago
Updated: 4 months ago
Last pushed: 4 months ago
Last synced: 4 months ago

Topics: bioinformatics, pipeline, plink, smoove, snakemake, snakemake-pipeline, structural-variation, structural-variation-calling, survivor, vep

Files

Readme

Dependencies

requirements.txt pypi

aioeasywebdav =2.4.0=py39hf3d152e_1001
aiohttp =3.7.4.post0=py39h3811e60_0
amply =0.1.4=py_0
appdirs =1.4.4=pyh9f0ad1d_0
async-timeout =3.0.1=py_1000
atk-1.0 =2.36.0=h3371d22_4
attmap =0.13.0=pyhd8ed1ab_0
attrs =21.2.0=pyhd8ed1ab_0
backports =1.0=py_2
backports.functools_lru_cache =1.6.4=pyhd8ed1ab_0
bcrypt =3.2.0=py39h3811e60_1
biopython =1.79=py39h3811e60_0
boto3 =1.18.44=pyhd8ed1ab_0
botocore =1.21.44=pyhd8ed1ab_0
brotlipy =0.7.0=py39h3811e60_1001
bzip2 =1.0.8=h7f98852_4
c-ares =1.17.2=h7f98852_0
ca-certificates =2021.5.30=ha878542_0
cachetools =4.2.2=pyhd8ed1ab_0
cairo =1.16.0=h6cf1ce9_1008
certifi =2021.5.30=py39hf3d152e_0
cffi =1.14.6=py39he32792d_0
chardet =4.0.0=py39hf3d152e_1
charset-normalizer =2.0.0=pyhd8ed1ab_0
coincbc =2.10.5=hcee13e7_1
colorama =0.4.4=pyh9f0ad1d_0
conda =4.10.3=py39hf3d152e_2
conda-package-handling =1.7.3=py39h3811e60_0
configargparse =1.5.2=pyhd8ed1ab_0
connection_pool =0.0.3=pyhd3deb0d_0
cryptography =3.4.7=py39hbca0aa6_0
cycler =0.10.0=py_2
datrie =0.8.2=py39h3811e60_2
decorator =4.4.2=py_0
docutils =0.17.1=py39hf3d152e_0
dropbox =11.19.0=pyhd8ed1ab_0
expat =2.4.1=h9c3ff4c_0
fftw =3.3.10=nompi_hcdd671c_100
filechunkio =1.8=py_2
filelock =3.0.12=pyh9f0ad1d_0
font-ttf-dejavu-sans-mono =2.37=hab24e00_0
font-ttf-inconsolata =3.000=h77eed37_0
font-ttf-source-code-pro =2.038=h77eed37_0
font-ttf-ubuntu =0.83=hab24e00_0
fontconfig =2.13.1=hba837de_1005
fonts-conda-ecosystem =1=0
fonts-conda-forge =1=0
freetype =2.10.4=h0708190_1
fribidi =1.0.10=h36c2ea0_0
ftputil =5.0.1=pyhd8ed1ab_0
gdk-pixbuf =2.42.6=h04a7f16_0
gettext =0.19.8.1=h0b5b191_1005
ghostscript =9.18=1
giflib =5.2.1=h36c2ea0_2
gitdb =4.0.7=pyhd8ed1ab_0
gitpython =3.1.23=pyhd8ed1ab_1
google-api-core =1.31.2=pyhd8ed1ab_0
google-api-python-client =2.21.0=pyhd8ed1ab_0
google-auth =1.35.0=pyh6c4a22f_0
google-auth-httplib2 =0.1.0=pyhd8ed1ab_0
google-cloud-core =1.7.2=pyh6c4a22f_0
google-cloud-storage =1.19.0=py_0
google-crc32c =1.1.2=py39hb81f231_0
google-resumable-media =2.0.2=pyh6c4a22f_0
googleapis-common-protos =1.53.0=py39hf3d152e_0
graphite2 =1.3.13=h58526e2_1001
graphviz =2.49.0=h85b4f2f_0
grpcio =1.38.1=py39hff7568b_0
gtk2 =2.24.33=h539f30e_1
gts =0.7.6=h64030ff_2
harfbuzz =2.9.1=h83ec7ef_0
httplib2 =0.19.1=pyhd8ed1ab_0
icu =68.1=h58526e2_0
idna =3.1=pyhd3deb0d_0
imagemagick =7.1.0_8=pl5321hb118871_0
importlib-metadata =4.8.1=py39hf3d152e_0
iniconfig =1.1.1=pyh9f0ad1d_0
ipython_genutils =0.2.0=py_1
jbig =2.1=h7f98852_2003
jinja2 =3.0.1=pyhd8ed1ab_0
jmespath =0.10.0=pyh9f0ad1d_0
jpeg =9d=h36c2ea0_0
jsonschema =3.2.0=pyhd8ed1ab_3
jupyter_core =4.8.1=py39hf3d152e_0
kiwisolver =1.3.2=py39h1a9c180_0
krb5 =1.19.2=hcc1bbae_2
lcms2 =2.12=hddcbb42_0
ld_impl_linux-64 =2.36.1=hea4e1c9_2
lerc =2.2.1=h9c3ff4c_0
libarchive =3.5.2=hccf745f_1
libblas =3.9.0=11_linux64_openblas
libcblas =3.9.0=11_linux64_openblas
libcrc32c =1.1.1=h9c3ff4c_2
libcurl =7.79.1=h2574ce0_1
libdeflate =1.7=h7f98852_5
libedit =3.1.20191231=he28a2e2_2
libev =4.33=h516909a_1
libffi =3.3=h58526e2_2
libgcc =7.2.0=h69d50b8_2
libgcc-ng =11.2.0=h1d223b6_8
libgd =2.3.2=h78a0170_0
libgfortran-ng =11.2.0=h69a702a_8
libgfortran5 =11.2.0=h5c6108e_8
libglib =2.68.4=h3e27bee_0
libgomp =11.2.0=h1d223b6_8
libiconv =1.16=h516909a_0
liblapack =3.9.0=11_linux64_openblas
libnghttp2 =1.43.0=h812cca2_1
libopenblas =0.3.17=pthreads_h8fe5266_1
libpng =1.6.37=h21135ba_2
libprotobuf =3.18.0=h780b84a_0
librsvg =2.50.7=hc3c00ef_0
libsodium =1.0.18=h36c2ea0_1
libsolv =0.7.19=h780b84a_5
libssh2 =1.10.0=ha56f1ee_2
libstdcxx-ng =11.2.0=he4da1e4_8
libtiff =4.3.0=hf544144_1
libtool =2.4.6=h9c3ff4c_1008
libuuid =2.32.1=h7f98852_1000
libwebp =1.2.1=h3452ae3_0
libwebp-base =1.2.1=h7f98852_0
libxcb =1.13=h7f98852_1003
libxml2 =2.9.12=h72842e0_0
logmuse =0.2.6=pyh8c360ce_0
lz4-c =1.9.3=h9c3ff4c_1
lzo =2.10=h516909a_1000
mamba =0.16.0=py39h951de11_0
markupsafe =2.0.1=py39h3811e60_0
matplotlib-base =3.4.3=py39h2fa2bec_0
more-itertools =8.10.0=pyhd8ed1ab_0
multidict =5.1.0=py39h3811e60_1
nbformat =5.1.3=pyhd8ed1ab_0
ncurses =6.2=h58526e2_4
networkx =2.6.3=pyhd8ed1ab_0
numpy =1.21.2=py39hdbf815f_0
oauth2client =4.1.3=py_0
olefile =0.46=pyh9f0ad1d_1
openjpeg =2.4.0=hb52868f_1
openssl =1.1.1l=h7f98852_0
packaging =21.0=pyhd8ed1ab_0
pandas =1.3.3=py39hde0f152_0
pango =1.48.10=hb8ff022_0
paramiko =2.7.2=pyh9f0ad1d_0
pcre =8.45=h9c3ff4c_0
peppy =0.31.1=pyhd8ed1ab_0
perl =5.32.1=0_h7f98852_perl5
pillow =8.3.2=py39ha612740_0
pip =21.2.4=pyhd8ed1ab_0
pixman =0.40.0=h36c2ea0_0
pkg-config =0.29.2=h36c2ea0_1008
pluggy =1.0.0=py39hf3d152e_1
ply =3.11=py_1
prettytable =2.2.0=pyhd8ed1ab_0
protobuf =3.18.0=py39he80948d_0
psutil =5.8.0=py39h3811e60_1
pthread-stubs =0.4=h36c2ea0_1001
pulp =2.5.0=py39hf3d152e_0
py =1.10.0=pyhd3deb0d_0
pyasn1 =0.4.8=py_0
pyasn1-modules =0.2.7=py_0
pycosat =0.6.3=py39h3811e60_1006
pycparser =2.20=pyh9f0ad1d_2
pygments =2.10.0=pyhd8ed1ab_0
pygraphviz =1.7=py39h78163bd_0
pynacl =1.4.0=py39h3811e60_2
pyopenssl =20.0.1=pyhd8ed1ab_0
pyparsing =2.4.7=pyh9f0ad1d_0
pyrsistent =0.17.3=py39h3811e60_2
pysftp =0.2.9=py_1
pysocks =1.7.1=py39hf3d152e_3
pytest =6.2.5=py39hf3d152e_0
python =3.9.6=h49503c6_1_cpython
python-dateutil =2.8.2=pyhd8ed1ab_0
python-irodsclient =1.0.0=pyhd8ed1ab_0
python_abi =3.9=2_cp39
pytz =2021.1=pyhd8ed1ab_0
pyu2f =0.1.5=pyhd8ed1ab_0
pyvcf =0.6.8=py39hde42818_1002
pyyaml =5.4.1=py39h3811e60_1
ratelimiter =1.2.0=py_1002
readline =8.1=h46c0cb4_0
reproc =14.2.3=h7f98852_0
reproc-cpp =14.2.3=h9c3ff4c_0
requests =2.26.0=pyhd8ed1ab_0
rsa =4.7.2=pyh44b312d_0
ruamel_yaml =0.15.80=py39h3811e60_1004
s3transfer =0.5.0=pyhd8ed1ab_0
scipy =1.7.1=py39hee8e79c_0
setuptools =58.0.4=py39hf3d152e_0
simplejson =3.17.5=py39h3811e60_0
six =1.16.0=pyh6c4a22f_0
slacker =0.14.0=py_0
smart_open =5.2.1=pyhd8ed1ab_0
smmap =3.0.5=pyh44b312d_0
snakemake =6.7.0=hdfd78af_0
snakemake-minimal =6.7.0=pyhdfd78af_0
sqlite =3.36.0=h9cd32fc_1
stone =3.2.1=pyhd8ed1ab_0
stopit =1.1.2=py_0
tabulate =0.8.9=pyhd8ed1ab_0
tk =8.6.11=h27826a3_1
toml =0.10.2=pyhd8ed1ab_0
toposort =1.6=pyhd8ed1ab_0
tornado =6.1=py39h3811e60_1
tqdm =4.62.3=pyhd8ed1ab_0
traitlets =5.1.0=pyhd8ed1ab_0
typing-extensions =3.10.0.0=hd8ed1ab_0
typing_extensions =3.10.0.0=pyha770c72_0
tzdata =2021a=he74cb21_1
ubiquerg =0.6.1=pyh9f0ad1d_0
uritemplate =3.0.1=py_0
urllib3 =1.26.6=pyhd8ed1ab_0
veracitools =0.1.3=py_0
wcwidth =0.2.5=pyh9f0ad1d_2
wheel =0.37.0=pyhd8ed1ab_1
wrapt =1.12.1=py39h3811e60_3
xmlrunner =1.7.7=py_0
xorg-kbproto =1.0.7=h7f98852_1002
xorg-libice =1.0.10=h7f98852_0
xorg-libsm =1.2.3=hd9c2040_1000
xorg-libx11 =1.7.2=h7f98852_0
xorg-libxau =1.0.9=h7f98852_0
xorg-libxdmcp =1.1.3=h7f98852_0
xorg-libxext =1.3.4=h7f98852_1
xorg-libxrender =0.9.10=h7f98852_1003
xorg-libxt =1.2.1=h7f98852_2
xorg-renderproto =0.11.1=h7f98852_1002
xorg-xextproto =7.3.0=h7f98852_1002
xorg-xproto =7.0.31=h7f98852_1007
xz =5.2.5=h516909a_1
yaml =0.2.5=h516909a_0
yarl =1.6.3=py39h3811e60_2
zipp =3.5.0=pyhd8ed1ab_0
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zstd =1.5.0=ha95c52a_0