Loads BioGRID data into NDEx
Project description
NDEx BioGRID Content Loader
Python application for loading BioGRID data into NDEx.
This tool downloads and unpacks the BioGRID files below
Dependencies
Compatibility
Python 3.3+
Installation
git clone https://github.com/ndexcontent/ndexbiogridloader
cd ndexbiogridloader
make dist
pip install dist/ndexloadbiogrid*whl
Run make command with no arguments to see other build/deploy options including creation of Docker image
make
Output:
clean remove all build, test, coverage and Python artifacts
clean-build remove build artifacts
clean-pyc remove Python file artifacts
clean-test remove test and coverage artifacts
lint check style with flake8
test run tests quickly with the default Python
test-all run tests on every Python version with tox
coverage check code coverage quickly with the default Python
docs generate Sphinx HTML documentation, including API docs
servedocs compile the docs watching for changes
testrelease package and upload a TEST release
release package and upload a release
dist builds source and wheel package
install install the package to the active Python's site-packages
dockerbuild build docker image and store in local repository
dockerpush push image to dockerhub
Configuration
The ndexloadbiogrid.py requires a configuration file in the following format be created.
The default path for this configuration is ~/.ndexutils.conf
but can be overridden with
--conf
flag.
Format of configuration file:
[<value in --profile (default ndexbiogridloader)>]
user = <NDEx username>
password = <NDEx password>
server = <NDEx server(omit http) ie public.ndexbio.org>
Example of default configuration file:
[ndexbiogridloader]
user = joe123
password = somepassword123
server = dev.ndexbio.org
Needed files
TODO: Add description of needed files
Usage
For information invoke ndexloadbiogrid.py -h
The command shown below will download the default version of BioGRID files (3.5.175) to the working
directory biogrid_data
, will generate CX networks in this directory, and then upload these networks
to default account specified in [ndexbiogridloader]
section of default configuration file:
ndexloadbiogrid.py biogrid_data
Via Docker
Example usage
TODO: Add information about example usage
docker run -v `pwd`:`pwd` -w `pwd` vrynkov/ndexbiogridloader:0.1.0 ndexloadbiogrid.py --conf conf # TODO Add other needed arguments here
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.1.1 (2019-08-23)
First release on PyPI.
Project details
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