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Open Source Science

https://github.com/common-workflow-language/cwldep

Common Workflow Language dependency manager

https://github.com/common-workflow-language/cwldep

Science Score: 26.0%

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
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary

Keywords from Contributors

workflow-engine bioinformatics cwl genomics common-workflow-language workflows
Last synced: 11 months ago · JSON representation

Repository

Common Workflow Language dependency manager

Basic Info
  • Host: GitHub
  • Owner: common-workflow-language
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Size: 31.3 KB
Statistics
  • Stars: 10
  • Watchers: 11
  • Forks: 3
  • Open Issues: 1
  • Releases: 0
Created about 8 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

Common Workflow Language dependency manager

This tool helps you to import tools and workflows from other sources for use in your own workflow.

Setup

It is highly recommended to setup virtual environment before installing cwldep:

virtualenv -p python2 venv # Create a virtual environment, can use `python3` as well source venv/bin/activate # Activate environment before installing `cwldep`

Install from PyPi:

pip install cwldep

Install from source: git clone https://github.com/common-workflow-language/cwldep.git # clone cwldep repo cd cwldep # Switch to source directory python setup.py install cwldep -h # Check if the installation works correctly

Adding file dependencies

cwldep add myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl

This will download the CWL file and its dependencies to raw.githubusercontent.com/common-workflow-language/workflows/master/tools

Include it in your workflow as a relative file reference:

steps: step1: in: ... out: ... run: raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl

Changing the install target

cwldep add --install-to samtools myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl

Using archives

You can also import archives (.tar.gz, .tar.bz2, and .zip):

cwldep add myfile.cwl https://github.com/common-workflow-language/workflows/archive/draft2.tar.gz

This will download and extract to the local directory github.com/common-workflow-language/workflows/archive

Using git upstream

You can also import git repositories:

cwldep add myfile.cwl https://github.com/common-workflow-language/workflows

This will clone into the local directory github.com/common-workflow-language/workflows

cwldep add --set-version=draft-2 myfile.cwl https://github.com/common-workflow-language/workflows

Installing dependencies

This will install any dependencies listed in myfile.cwl

cwldep install myfile.cwl

Checking if upstream dependencies have changed

This will report if the upstream dependencies listed in myfile.cwl have changed

cwldep check myfile.cwl

Updating dependencies

This will install updated dependencies:

cwldep update myfile.cwl

Deleting unreferenced dependencies

This will delete any dependencies listed in the ".dep.lock" file that are not referenced by myfile.cwl.

cwldep clean myfile.cwl

Owner

  • Name: Common Workflow Language
  • Login: common-workflow-language
  • Kind: organization

GitHub Events

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

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 24
  • Total Committers: 4
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.417
Top Committers
Name Email Commits
Peter Amstutz p****z@v****m 14
John Bradley j****8@g****m 8
dependabot-preview[bot] 2****]@u****m 1
Peter Amstutz p****z@c****m 1
Committer Domains (Top 20 + Academic)
curii.com: 1 veritasgenetics.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 1
  • Total pull requests: 5
  • Average time to close issues: 3 days
  • Average time to close pull requests: 31 minutes
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • Bot issues: 1
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dependabot-preview[bot] (1)
Pull Request Authors
  • johnbradley (3)
  • TrellixVulnTeam (1)
  • dependabot-preview[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 14 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 2
pypi.org: cwldep

Common workflow language dependency manager

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 14 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 16.8%
Stargazers count: 17.7%
Dependent repos count: 21.7%
Average: 25.7%
Downloads: 62.4%
Maintainers (2)
mcrusoe tetron
Last synced: 11 months ago

Dependencies

setup.py pypi
  • cwltool *
  • python-dateutil *