cellmaps-ppidownloader 0.1.0a2

Downloads APMS edgelist data for CM4AI MuSIC pipeline

cellmaps_ppidownloader

Downloads AP-MS data needed for CM4AI MuSIC pipeline

• Free software: MIT license

• Documentation: https://cellmaps-ppidownloader.readthedocs.io.

Dependencies

• TODO add

Compatibility

• Python 3.8+

Installation

git clone https://github.com/idekerlab/cellmaps_ppidownloader
cd cellmaps_ppidownloader
make dist
pip install dist/cellmaps_ppidownloadercmd*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

Needed files

TODO: Add description of needed files

Usage

For information invoke cellmaps_ppidownloadercmd.py -h

Example usage

TODO: Add information about example usage

# Download bioplex 1.0 interaction list and baitlist
# curl commands below do just that, but if not installed download
# the files from https://bioplex.hms.harvard.edu/interactions.php
# via a browser
curl -O https://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v2.tsv
curl -O https://bioplex.hms.harvard.edu/data/BioPlex_1p0_293T_baitList.tsv

cellmaps_ppidownloadercmd.py # TODO Add other needed arguments here

Via Docker

Example usage

TODO: Add information about example usage

docker run -v `pwd`:`pwd` -w `pwd` idekerlab/cellmaps_ppidownloader:0.1.0 cellmaps_ppidownloadercmd.py # TODO Add other needed arguments here

Credits

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

History

0.1.0 (2023-05-15)

• First release on PyPI.