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GitHub / imperial-genomics-facility / data-management-python

Python library for running data analysis pipelines for IGF team

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/imperial-genomics-facility%2Fdata-management-python

Stars: 4
Forks: 2
Open Issues: 8

License: apache-2.0
Language: Python
Repo Size: 2.98 MB
Dependencies: 174

Created: about 7 years ago
Updated: almost 2 years ago
Last pushed: 10 days ago
Last synced: 9 days ago

Topics: illumina, mysql, ngs, pandas, python, sqlalchemy

Files

Readme

Dependencies

requirements.txt pypi

Babel ==2.8.0
Flask ==1.1.2
Flask-Admin ==1.5.4
Flask-AppBuilder ==2.3.4
Flask-Babel ==1.0.0
Flask-Caching ==1.3.3
Flask-JWT-Extended ==3.24.1
Flask-Login ==0.4.1
Flask-SQLAlchemy ==2.4.4
Flask-WTF ==0.14.3
Jinja2 ==2.11.2
Mako ==1.1.3
Markdown ==2.6.11
MarkupSafe ==1.1.1
PyJWT ==1.7.1
PyMySQL ==0.9.2
PyNaCl ==1.4.0
PyYAML ==5.3.1
Pygments ==2.6.1
SQLAlchemy ==1.3.18
SQLAlchemy-JSONField ==0.9.0
SQLAlchemy-Utils ==0.36.8
Sphinx ==3.2.1
WTForms ==2.3.3
Werkzeug ==0.16.1
alabaster ==0.7.12
alembic ==1.4.2
amqp ==2.6.1
apache-airflow ==1.10.12
apispec ==1.3.3
argcomplete ==1.12.0
asana ==0.10.3
atlassian-python-api ==3.14.0
attrs ==19.3.0
bcrypt ==3.2.0
beautifulsoup4 ==4.9.3
billiard ==3.6.3.0
bs4 ==0.0.1
cached-property ==1.5.1
cachetools ==4.1.1
cattrs ==1.0.0
celery ==4.4.7
certifi ==2020.6.20
cffi ==1.14.2
chardet ==3.0.4
click ==6.7
colorama ==0.4.3
colorlog ==4.0.2
configparser ==3.5.3
coverage ==5.3
coveralls ==1.3.0
croniter ==0.3.34
cryptography ==3.0
defusedxml ==0.6.0
dill ==0.3.2
dnspython ==1.16.0
docopt ==0.6.2
docutils ==0.16
email-validator ==1.1.1
flask-swagger ==0.2.14
flower ==0.9.5
funcsigs ==1.0.2
future ==0.18.2
graphviz ==0.14.1
grpc-google-iam-v1 ==0.12.3
grpcio ==1.31.0
grpcio-gcp ==0.2.2
gunicorn ==20.0.4
gviz-api ==1.9.0
html5lib ==1.0.1
httplib2 ==0.18.1
humanize ==2.6.0
idna ==2.10
imagesize ==1.2.0
importlib-metadata ==1.7.0
install ==1.3.4
iso8601 ==0.1.12
itsdangerous ==1.1.0
json-merge-patch ==0.2
jsonschema ==3.2.0
kombu ==4.6.11
lazy-object-proxy ==1.5.1
linecache2 ==1.0.0
lockfile ==0.12.2
lxml ==4.2.4
marshmallow ==2.21.0
marshmallow-enum ==1.5.1
marshmallow-sqlalchemy ==0.23.1
matplotlib ==3.3.2
natsort ==7.0.1
numpy ==1.19.1
oauthlib ==3.1.0
packaging ==20.4
pandas ==1.1.0
pandas-gbq ==0.13.2
paramiko ==2.7.1
pendulum ==1.4.4
prison ==0.1.3
prometheus-client ==0.8.0
protobuf ==3.13.0
psutil ==5.7.2
psycopg2-binary ==2.8.5
pyOpenSSL ==19.1.0
pyasn1 ==0.4.8
pyasn1-modules ==0.2.8
pycparser ==2.20
pydata-google-auth ==1.1.0
pyparsing ==2.4.7
pyrsistent ==0.16.0
python-daemon ==2.2.4
python-dateutil ==2.8.1
python-editor ==1.0.4
python-nvd3 ==0.15.0
python-slugify ==4.0.1
python3-openid ==3.2.0
pytz ==2020.1
pytzdata ==2020.1
redis ==3.5.3
requests ==2.24.0
requests-oauthlib ==1.3.0
rsa ==4.6
semver ==2.10.2
setproctitle ==1.1.10
six ==1.15.0
slackclient ==1.3.2
snowballstemmer ==2.0.0
soupsieve ==2.0.1
sphinx-rtd-theme ==0.4.3
sphinx_rtd_theme ==0.4.3
sphinxcontrib-applehelp ==1.0.2
sphinxcontrib-devhelp ==1.0.2
sphinxcontrib-htmlhelp ==1.0.3
sphinxcontrib-jsmath ==1.0.1
sphinxcontrib-qthelp ==1.0.3
sphinxcontrib-serializinghtml ==1.1.4
spython ==0.0.85
sshtunnel ==0.2.2
tabulate ==0.8.7
tenacity ==4.12.0
text-unidecode ==1.3
thrift ==0.13.0
tornado ==5.1.1
traceback2 ==1.4.0
typing ==3.7.4.3
typing-extensions ==3.7.4.2
tzlocal ==1.5.1
unicodecsv ==0.14.1
unittest2 ==1.1.0
uritemplate ==3.0.1
urllib3 ==1.25.10
vine ==1.3.0
webencodings ==0.5.1
websocket-client ==0.54.0
xlrd ==1.1.0
zipp ==3.1.0
zope.deprecation ==4.4.0

.github/workflows/python-app.yml actions

actions/checkout v3 composite
actions/setup-python v3 composite

doc/environment.yaml conda

pip
python 3.6.*

environment.yaml conda

ca-certificates 2021.10.8.*
ld_impl_linux-64
libffi
libgcc-ng
libgomp 11.2.0.*
libnsl 2.0.0.*
libstdcxx-ng 11.2.0.*
libzlib 1.2.11.*
openssl 3.0.0.*
pip 21.3.1.*
pip
python 3.7.12.*
readline 8.1.*
sqlite 3.37.0