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cellprofiler-on-terra

Run CellProfiler on Terra. Contains workflows that enable a full end-to-end Cell Painting pipeline.

https://github.com/broadinstitute/cellprofiler-on-terra

Science Score: 52.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization broadinstitute has institutional domain (www.broadinstitute.org)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Run CellProfiler on Terra. Contains workflows that enable a full end-to-end Cell Painting pipeline.

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: bsd-3-clause
  • Language: WDL
  • Default Branch: main
  • Homepage:
  • Size: 187 KB
Statistics
  • Stars: 8
  • Watchers: 3
  • Forks: 5
  • Open Issues: 13
  • Releases: 3
Created over 5 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

CellProfiler on Terra

WDL workflows and scripts for running a CellProfiler pipeline on Google Cloud hardware. Includes workflows for all steps of a full Cell Painting pipeline.

Works well in Terra, and will also work on any Cromwell server that can run WDLs. Currently specific to a Google Cloud backend. (We are open to supporting more backends, specifically cloud storage locations, in the future, including AWS and Azure.)

You can see these workflows in action and try them yourself in Terra workspace cellpainting!

Three pipelines:

  1. Cell Painting
- All the workflows necessary to run an end-to-end Cell Painting pipeline, 
starting with raw images and ending with extracted features, both in database 
format and aggregated as CSV files.
- Appropriate for datasets of arbitrary size.
- Scatters the time-consuming analysis steps over many VMs in parallel. 
By default, a dataset is split into individual wells, and each well is run 
on a separate VM.
  1. Cytominer
- Run the [`cytominer-database`](https://github.com/cytomining/cytominer-database) 
ingest step to create a SQLite database containing all the extracted features.
- Run the aggregation step from [`pycytominer`](https://github.com/cytomining/pycytominer) 
to create CSV files.
  1. CellProfiler (distributed or single VM)
- A single WDL workflow that runs a 
[CellProfiler `.cppipe` pipeline](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.1/help/pipelines_building.html) 
on a dataset.

How to run these workflows yourself

These workflows are all publicly available, and hosted in Dockstore. From there, you can import and run the workflows in Terra or any other place you like to run WDL workflows.

You can clone the Terra workspace cellpainting, which is conveniently preconfigured to run on three plates of sample data, if you just want to give it a try.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

Citation (CITATION.cff) 

cff-version: 1.2.0
title: Cellprofiler-on-Terra
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Carmen
    family-names: Diaz Verdugo
    email: cdiazver@broadinstitute.org
    orcid: 'https://orcid.org/0000-0002-1378-8592'
  - given-names: Stephen Jordan
    family-names: Fleming
    email: sfleming@broadinstitute.org
    orcid: 'https://orcid.org/0000-0002-1885-4405'
  - given-names: Nicole
    family-names: Deflaux
    email: deflaux@verily.com
    orcid: 'https://orcid.org/0000-0002-9421-8048'
url: "https://github.com/broadinstitute/cellprofiler-on-Terra"

GitHub Events

Total
  • Watch event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Fork event: 1

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 8
proxy.golang.org: github.com/broadinstitute/cellprofiler-on-terra
  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.9%
Last synced: 10 months ago
proxy.golang.org: github.com/broadinstitute/cellprofiler-on-Terra
  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.9%
Last synced: 10 months ago

Dependencies

.github/workflows/miniwdl_check.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/womtool_validate.yml actions
  • ./.github/actions/install-cromwell * composite
  • actions/checkout v3 composite
docker/Dockerfile docker
  • python 3.7-slim build
pipelines/mining/docker/Dockerfile docker
  • python 3.7 build
pipelines/mining/docker_jumpcp/Dockerfile docker
  • python 3.7 build
.github/actions/install-cromwell/action.yml actions