https://github.com/nanxstats/cwl-upgrader
Shiny app to upgrade Common Workflow Language (CWL) apps from sbg:draft2 to v1.0
https://github.com/nanxstats/cwl-upgrader
bioinformatics common-workflow-language cwl reticulate shiny-apps
Last synced: about 1 month ago
JSON representation
Shiny app to upgrade Common Workflow Language (CWL) apps from sbg:draft2 to v1.0
- Host: GitHub
- URL: https://github.com/nanxstats/cwl-upgrader
- Owner: nanxstats
- License: agpl-3.0
- Created: 2020-02-17T19:50:16.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-05-09T03:27:04.000Z (almost 5 years ago)
- Last Synced: 2025-03-05T22:11:50.927Z (about 2 months ago)
- Topics: bioinformatics, common-workflow-language, cwl, reticulate, shiny-apps
- Language: R
- Homepage: https://nanx.app/cwl-upgrader/
- Size: 1.47 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# cwl-upgrader
A shiny app to upgrade Common Workflow Language (CWL) apps from `sbg:draft2` to `v1.0` using the Python package sevenbridges-cwl-draft2-upgrader.
## Dependencies
This app uses [reticulate](https://rstudio.github.io/reticulate/) to call Python and the Python package [sevenbridges-cwl-draft2-upgrader](https://github.com/sbg/sevenbridges-cwl-draft2-upgrader). 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("sevenbridges-cwl-draft2-upgrader"), 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-exploder](https://github.com/nanxstats/cwl-exploder) - Shiny app to unpack monolithic CWL workflows and split them into smaller components.
## Copyright
© 2020 Seven Bridges Genomics, Inc. All rights reserved.
This project is licensed under the [GNU Affero General Public License v3](LICENSE).