Toolchest R Client

Toolchest runs computational biology software in the cloud with just a few lines of code. You can call Toolchest from anywhere Python or R runs, using input files located on your computer or S3.

This package contains the R client for using Toolchest. For the Python client, see here.

Documentation & User Guide

Usage

Using Toolchest is as simple as:

1. installing the client (listed as the toolchest package)

2. configuring Toolchest with your given Toolchest key:

toolchest::set_key("YOUR_TOOLCHEST_KEY")

3. running the following:

toolchest::tool_name(tool_args)

tool_name is the name of the desired tool, and tool_args is a string containing any additional arguments to be passed to the function.

Input and output paths can be specified as well:

toolchest::tool_name(
    tool_args,
    inputs = "/path/to/input",
    output_path = "/path/to/output"
)

A list of tools can be found on the Toolchest docs page.

Installation

You can install the development version from GitHub with:

# install.packages("devtools") # uncomment to install devtools (prereq package)
devtools::install_github("trytoolchest/toolchest-client-r", dependencies = TRUE)
library(toolchest)

R dependencies

The R client requires the reticulate package, version 1.25 or greater.

Install or update reticulate with:

install.packages("reticulate")

Python requirements

The R client requires a version of Python 3.7 or greater.

A compatible version will automatically be installed via miniconda or pyenv, using R’s reticulate package.

Troubleshooting

For more details, see the INSTALL page. If you’re having trouble with installation, consult the page and/or contact Toolchest directly.

Configuration

To use Toolchest, you must have an authentication key.

Contact Toolchest if:

• you need a key
• you’ve forgotten your key
• the key is producing authentication errors.

Once you have your key, set the environment variable TOOLCHEST_KEY to the key value:

toolchest::set_key("YOUR_TOOLCHEST_KEY")

.Renviron

To prevent having to load the TOOLCHEST_KEY value every time R starts, you can add the value to your .Renviron file.

If you don’t know what this is or if you’re unsure if this file exists, use Sys.getenv("R_USER") in R to find the location of your home folder, and create a file named .Renviron. Then, add the following line to it:

TOOLCHEST_KEY = YOUR_TOOLCHEST_KEY

where YOUR_TOOLCHEST_KEY is the value of your Toolchest key.

Note that these changes must be loaded in order to take effect. This automatically happens at the start of each R session.

After adding/editing an .Renviron file during your R session, you can proceed to load .Renviron into your current R session as follows:

readRenviron("~/.Renviron")

Help / R Studio Documentation

Visit our main docs page at docs.trytoolchest.com.

Documentation for each tool can also be accessed within R, just like any other function in an R package. For help on how to use an individual tool, use either of the following:

• help(tool_name)
• ?toolchest::tool_name (or simply ?tool_name)