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Open Source Science

https://github.com/broadinstitute/depmap-omics-long-read-rna

https://github.com/broadinstitute/depmap-omics-long-read-rna

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • Language: Python
  • Default Branch: main
  • Size: 729 KB
Statistics
  • Stars: 0
  • Watchers: 8
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed 11 months ago
Metadata Files
Readme

README.md

Depmap Omics Long Read RNA

This repository contains WDL workflows and a Python module to continuously run workflows on new RNA long read samples and sync BAM files between Terra and Gumbo.

Installation

  1. Install uv.

  2. Create a new virtualenv and install the project dependencies:

sh uv venv uv sync

  1. Copy env.dist into a new file .env and fill it out:
- `WOMTOOL_JAR` is the path to the .jar file downloaded from [https://github.com/broadinstitute/cromwell/releases](broadinstitute/cromwell)
- `FIRECLOUD_OWNERS` is a list of Terra users (email addresses or group names) that should be considered owners of workflow method configs

Credentials

Your GCP DEFAULT_APPLICATION_CREDENTIALS must already be configured in order to run commands.

Development

Configure your editor or IDE to automatically format your code with Ruff and check static types with Pyright by running uv run pyright.

Whenever possible, function/method arguments and return values should be validated with Pydantic or Pandera (if a data frame).

GraphQL code generation

This repo uses ariadne-codegen to generate the gumbo_gql_client module. It uses the folder of GraphQL queries (./gql) and the current GraphQL schema for a particular Gumbo environment to generate all of the Python classes, Pydantic models, and query/mutation methods for interacting with the Gumbo GraphQL Service. To regenerate the module using the current production schema:

shell HASURA_ADMIN_SECRET=... uv run ariadne-codegen --config ariadne-prod.toml

Scratch files

Some Python files in ./scratch are available to seed existing data (i.e. legacy uBAM files).

Owner

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

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Watch event: 1
  • Delete event: 3
  • Push event: 76
  • Pull request review event: 3
  • Pull request review comment event: 9
  • Pull request event: 13
  • Create event: 3
Last Year
  • Watch event: 1
  • Delete event: 3
  • Push event: 76
  • Pull request review event: 3
  • Pull request review comment event: 9
  • Pull request event: 13
  • Create event: 3

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 120
  • Total Committers: 1
  • Avg Commits per committer: 120.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 120
  • Committers: 1
  • Avg Commits per committer: 120.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Devin McCabe d****e@b****g 120
Committer Domains (Top 20 + Academic)
broadinstitute.org: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • hannharris (5)
  • dependabot[bot] (1)
  • dpmccabe (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Dependencies

poetry.lock pypi
  • 106 dependencies
pyproject.toml pypi
  • pyright ^1.1.382 develop
  • ruff 0.6.8 develop
  • ariadne-codegen ^0.14.0
  • functions-framework ^3.5.0
  • google-cloud-logging ^3.9.0
  • google-cloud-secret-manager ^2.20.2
  • google-cloud-storage ^2.14.0
  • nebelung ^1.3.0
  • numpy ^2.1.1
  • pandas ^2.2.3
  • pandera ^0.20.4
  • pyarrow ^18.0.0
  • pydantic ^2.9.2
  • python ^3.12
  • python-baseconv ^1.2.2
  • python-dotenv ^1.0.1
  • tqdm ^4.66.1
  • typer ^0.12.5
requirements.txt pypi
  • annotated-types ==0.7.0
  • anyio ==4.6.2.post1
  • ariadne-codegen ==0.14.0
  • astroid ==3.3.5
  • attrs ==24.2.0
  • autoflake ==2.3.1
  • black ==24.10.0
  • blinker ==1.8.2
  • cachetools ==5.5.0
  • certifi ==2024.8.30
  • cffi ==1.17.1
  • charset-normalizer ==3.4.0
  • click ==8.1.7
  • cloudevents ==1.11.0
  • colorama ==0.4.6
  • cryptography ==43.0.3
  • deprecated ==1.2.14
  • deprecation ==2.1.0
  • dill ==0.3.9
  • firecloud ==0.16.37
  • flask ==3.0.3
  • functions-framework ==3.8.1
  • google-api-core ==2.21.0
  • google-auth ==2.35.0
  • google-cloud-appengine-logging ==1.4.5
  • google-cloud-audit-log ==0.3.0
  • google-cloud-core ==2.4.1
  • google-cloud-logging ==3.11.3
  • google-cloud-secret-manager ==2.20.2
  • google-cloud-storage ==2.18.2
  • google-crc32c ==1.6.0
  • google-resumable-media ==2.7.2
  • googleapis-common-protos ==1.65.0
  • graphql-core ==3.2.5
  • grpc-google-iam-v1 ==0.13.1
  • grpcio ==1.67.0
  • grpcio-status ==1.67.0
  • gunicorn ==23.0.0
  • h11 ==0.14.0
  • httpcore ==1.0.6
  • httpx ==0.27.2
  • hypothesis ==6.115.3
  • idna ==3.10
  • importlib-metadata ==8.4.0
  • isort ==5.13.2
  • itsdangerous ==2.2.0
  • jinja2 ==3.1.4
  • markdown-it-py ==3.0.0
  • markupsafe ==3.0.2
  • mccabe ==0.7.0
  • mdurl ==0.1.2
  • multimethod ==1.10
  • mypy-extensions ==1.0.0
  • nebelung ==1.3.0
  • nose ==1.3.7
  • numpy ==2.1.2
  • opentelemetry-api ==1.27.0
  • packaging ==24.1
  • pandas ==2.2.3
  • pandera ==0.20.4
  • pathspec ==0.12.1
  • platformdirs ==4.3.6
  • proto-plus ==1.24.0
  • protobuf ==5.28.2
  • pyarrow ==18.0.0
  • pyasn1 ==0.6.1
  • pyasn1-modules ==0.4.1
  • pycparser ==2.22
  • pydantic ==2.9.2
  • pydantic-core ==2.23.4
  • pydot ==3.0.2
  • pyflakes ==3.2.0
  • pygithub ==2.4.0
  • pygments ==2.18.0
  • pyjwt ==2.9.0
  • pylint ==3.3.1
  • pynacl ==1.5.0
  • pyparsing ==3.2.0
  • python-baseconv ==1.2.2
  • python-dateutil ==2.9.0.post0
  • python-dotenv ==1.0.1
  • pytz ==2024.2
  • requests ==2.31.0
  • rich ==13.9.3
  • rsa ==4.9
  • setuptools ==75.2.0
  • shellingham ==1.5.4
  • six ==1.16.0
  • sniffio ==1.3.1
  • sortedcontainers ==2.4.0
  • toml ==0.10.2
  • tomlkit ==0.13.2
  • tqdm ==4.66.5
  • typeguard ==4.3.0
  • typer ==0.12.5
  • typing-extensions ==4.12.2
  • typing-inspect ==0.9.0
  • tzdata ==2024.2
  • urllib3 ==2.2.3
  • watchdog ==5.0.3
  • werkzeug ==3.0.4
  • wrapt ==1.16.0
  • zipp ==3.20.2