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A toolbox to work with R projects on Renku

Project description

http://img.shields.io/badge/license-MIT-brightgreen.svg https://img.shields.io/github/v/release/auwerxlab/renku-r-tools

Renku-r-tools is a small python package that provides a CLI to setup R projects on Renku.

Features:

  • Link the packrat libraries of a R project to another location. This is useful when packrat libraries are located on the docker image.

Installation

The latest release is available on PyPI and can be installed using pip:

$ pip install renku-r-tools

Isolated environments using pipx

Install and execute renku-r-tools in an isolated environment using pipx.

Install pipx and make sure that the $PATH is correctly configured.

$ python3 -m pip install --user pipx
$ pipx ensurepath

Once pipx is installed use following command to install renku-r-tools.

$ pipx install renku-r-tools
$ which renku-r-tools
~/.local/bin/renku-r-tools

Usage

renku-r ln_packrat_lib

Usage: renku-r ln-packrat-lib [OPTIONS]

  Link packrat libraries to another location.

Options:
  -p, --proj_dir TEXT  R project main directory path. Use absolute path.
                       [required]
  -s, --source TEXT    Main directory path of the new packrat libraries
                       source. Use absolute path.  [default:
                       /home/rstudio/packrat; required]
  --help               Show this message and exit.

Example:

$ renku-r ln_packrat_lib -p <your_R_project_main_directory_path> -s <your_new_packrat_library_path>

Project details


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