Runs full Cell Maps pipeline
Project description
Cell Maps Pipeline
Free software: MIT license
Documentation: https://cellmaps-pipeline.readthedocs.io.
Source code: https://github.com/idekerlab/cellmaps_pipeline
Dependencies
cellmaps_utils (v. 0.3.0a1)
cellmaps_imagedownloader (v. 0.1.0)
cellmaps_ppidownloader (v. 0.1.0)
cellmaps_image_embedding (v. 0.1.0)
cellmaps_ppi_embedding (v. 0.2.0)
cellmaps_coembedding (v. 0.1.0)
cellmaps_generate_hierarchy (v. 0.1.0a20)
cellmaps_hierarchyeval (v. 0.1.0a8)
networkx (v. >=2.8,<2.9)
scipy (v. <1.13.0)
tqdm (v. 4.66.2)
Compatibility
Python 3.8+
OS Requirements
This package is supported for macOS and Linux. The package has been tested on the following systems:
macOS: Ventura (13.5)
Linux: Rocky Linux 8
Installation
Install from PyPi
pip install cellmaps_pipeline
Install from Github
git clone https://github.com/idekerlab/cellmaps_pipeline
cd cellmaps_pipeline
make dist
pip install dist/cellmaps_pipeline*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
Expected install time: ~30-40s
Before running tests, please install pip install -r requirements_dev.
For developers
To deploy development versions of this package
Below are steps to make changes to this code base, deploy, and then run against those changes.
Make changes
Modify code in this repo as desired
Build and deploy
# From base directory of this repo cellmaps_pipeline
pip uninstall cellmaps_pipeline -y ; make clean dist; pip install dist/cellmaps_pipeline*whl
Needed files
samples file: CSV file with list of IF images to download (see sample samples file in examples folder)
unique file: CSV file of unique samples (see sample unique file in examples folder)
bait list file: TSV file of baits used for AP-MS experiments
edge list file: TSV file of edges for protein interaction network
provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)
Usage
For information invoke cellmaps_pipelinecmd.py -h
Instruction for running cellmaps_pipeline
on your data can be found here.
Example usage (Demo)
cellmaps_pipelinecmd.py ./cellmaps_pipeline_outdir --samples examples/samples.csv --unique examples/unique.csv --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json
Expected run time for demo: ~55min (macOS: Ventura 13.5, M2 Processor)
Via Docker
Example usage
Coming soon...
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.1.0 (2023-05-22)
First release on PyPI.
Project details
Release history Release notifications | RSS feed
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