NDEx Cancer Hallmark networks from CPTAC at WikiPathways Enrichment Loader

Copies and converts Special collection of Cancer Hallmark networks from CPTAC at WikiPathways networks already loaded in NDEx so they can be used in Enrichment.

• Free software: BSD license
• Documentation: https://ndexcptacenrichloader.readthedocs.io.

Tools

• ndexloadcptacenrich.py -- Loads CPTAC into NDEx

Dependencies

• ndex2
• ndexutil

Compatibility

• Python 3.3+

Installation

git clone https://github.com/coleslaw481/ndexcptacenrichloader
cd ndexcptacenrichloader
make dist
pip install dist/ndexloadcptacenrich*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 ndexloadcptacenrich.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 ndexcptacenrichloader)>]

user = <NDEx username>
password = <NDEx password>
server = <NDEx server(omit http) ie public.ndexbio.org>
source_user = <NDEx username for source networks>
source_password = <NDEx password for source networks>
source_server = <NDEx server(omit http) ie public.ndexbio.org for source networks>
source_networkset = <id of network set containing networks>

Example configuration file

[ndexcptacenrichloader_dev]

user = joe123
password = somepassword123
server = dev.ndexbio.org
source_user = bob456
source_password = anotherpassword123
source_server = public.ndexbio.org
source_networkset = cf04cd21-b695-44b1-80c6-32952aaba2b9

Needed files

TODO: Add description of needed files

Usage

For information invoke ndexloadcptacenrich.py -h

Example usage

TODO: Add information about example usage

ndexloadcptacenrich.py # TODO Add other needed arguments here

Via Docker

Example usage

TODO: Add information about example usage

docker run -v `pwd`:`pwd` -w `pwd` coleslawndex/ndexcptacenrichloader:0.1.0 ndexloadcptacenrich.py --conf conf # TODO Add other needed arguments here

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.