https://github.com/nanxstats/sbpack-r

An R package to pack and upload CWL apps to Seven Bridges powered platforms
https://github.com/nanxstats/sbpack-r

bioinformatics common-workflow-language cwl reticulate

Last synced: 6 days ago
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An R package to pack and upload CWL apps to Seven Bridges powered platforms

• Host: GitHub
• URL: https://github.com/nanxstats/sbpack-r
• Owner: nanxstats
• Created: 2020-05-10T23:01:47.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-05-11T06:41:38.000Z (over 4 years ago)
• Last Synced: 2025-01-11T09:07:54.398Z (13 days ago)
• Topics: bioinformatics, common-workflow-language, cwl, reticulate
• Language: R
• Homepage: https://nanx.me/sbpack-r/
• Size: 48.8 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md

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README

        
# sbpack-r

[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)

sbpack-r is an R wrapper offering a functional interface for the Python package [sbpack](https://github.com/rabix/sbpack), which supports packing local or remote [Common Workflow Language](https://www.commonwl.org/) (CWL) apps and uploading them to Seven Bridges powered platforms.

## Installation

Install sbpack-r from GitHub:

```r

remotes::install_github("nanxstats/sbpack-r")

```

It depends on the Python package sbpack. Installed via pip:

```bash

pip3 install git+https://github.com/rabix/sbpack

```

## Usage

```r

reticulate::use_python("/usr/local/bin/python3")

library("sbpack")

"foo.cwl" %>% pack_to_file("bar.cwl")

"https://example.com/foo.cwl" %>% pack_to_file("bar.cwl")

"foo.cwl" %>% pack_to_sb("cgc", "user/project/app")

"https://example.com/foo.cwl" %>% pack_to_sb("cgc", "user/project/app")

```

## Developers

If you have already installed Python and sbpack, and want to develop sbpack-r in RStudio, simply create a file `.Rprofile` under the package directory and set the Python binary path (Homebrew Python 3 path example below):

```r

Sys.setenv(RETICULATE_PYTHON = "/usr/local/bin/python3")

```

The next time you open the project, the correct Python path and library path should be already set. For more technical details, see [reticulate Python version configuration](https://rstudio.github.io/reticulate/articles/versions.html).

## Copyright

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

This project is licensed under the GNU Affero General Public License v3.