https://github.com/nanxstats/cwl-exploder

Shiny app to unpack monolithic CWL workflows
https://github.com/nanxstats/cwl-exploder

bioinformatics common-workflow-language cwl reticulate shiny-apps

Last synced: 6 days ago
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Shiny app to unpack monolithic CWL workflows

• Host: GitHub
• URL: https://github.com/nanxstats/cwl-exploder
• Owner: nanxstats
• License: agpl-3.0
• Created: 2020-05-09T03:00:20.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-05-09T03:35:39.000Z (over 4 years ago)
• Last Synced: 2025-01-11T09:07:50.528Z (13 days ago)
• Topics: bioinformatics, common-workflow-language, cwl, reticulate, shiny-apps
• Language: R
• Homepage: https://nanx.app/cwl-exploder/
• Size: 1.07 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# cwl-exploder

A shiny app to unpack monolithic CWL workflows and split them into smaller components recursively using the Python package cwlformat.

## Dependencies

This app uses [reticulate](https://rstudio.github.io/reticulate/) to call Python and the Python package [cwlformat](https://github.com/rabix/cwl-format). Follow its readme to install the Python package either using pip or from GitHub.

After the Python package is installed, modify `.Rprofile` to give a hint to reticulate on where to find Python and the installed package. The default location is for a macOS Homebrew Python 3. Relaunch the RStudio session to use this profile.

If you encountered an error on unable to import the Python module, please consult the articles [Python Version Configuration](https://rstudio.github.io/reticulate/articles/versions.html) and [Installing Python Packages](https://rstudio.github.io/reticulate/articles/python_packages.html), then add a few lines to `server/wrapper.R` before `reticulate::import` to help reticulate locate the Python package. For example, if we use virtualenv:

```r

use_python("/your/path/to/bin/python3")

virtualenv_create("venv", python = "/your/path/to/bin/python3")

virtualenv_install("venv", packages = c("cwlformat"), ignore_installed = FALSE)

use_virtualenv("venv", required = TRUE)

```

## Related apps

- [cwl-formatter](https://github.com/nanxstats/cwl-formatter) - Shiny app to format Common Workflow Language apps.

- [cwl-upgrader](https://github.com/nanxstats/cwl-upgrader) - Shiny app to upgrade Common Workflow Language apps from sbg:draft2 to v1.0.

## Copyright

© 2020 Seven Bridges Genomics, Inc. All rights reserved.

This project is licensed under the [GNU Affero General Public License v3](LICENSE).