Loads GeneHancer database to NDEx
Project description
NDEx GeneHancer Content Loader
Loads GeneHancer database to NDEx
- Free software: MIT license
- Documentation: https://ndexgenehancerloader.readthedocs.io.
Compatibility
- Python 3.3+
Installation
git clone https://github.com/ceofy/ndexgenehancerloader cd ndexgenehancerloader make dist pip install dist/ndexloadgenehancer*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 ndexloadgenehancer.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 ndexgenehancerloader)>] user = <NDEx username> password = <NDEx password> server = <NDEx server(omit http) ie public.ndexbio.org>
Example configuration file
[ndexgenehancerloader_dev] user = joe123 password = somepassword123 server = dev.ndexbio.org
Needed files
TODO: Add description of needed files
Usage
For information invoke ndexloadgenehancer.py -h
Example usage
TODO: Add information about example usage
ndexloadgenehancer.py # TODO Add other needed arguments here
Via Docker
Example usage
TODO: Add information about example usage
docker run -v `pwd`:`pwd` -w `pwd` ceofy/ndexgenehancerloader:0.1.0 ndexloadgenehancer.py --conf conf # TODO Add other needed arguments here
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.1.0 (2019-10-23)
- First release on PyPI.
Project details
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