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 to call Python and the Python package 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 and Installing Python Packages, 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:

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 - Shiny app to format Common Workflow Language apps.
• 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.