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.
Using Toolchest is as simple as:
-
installing the client (listed as the
toolchest
package) -
configuring Toolchest with your given Toolchest key:
toolchest::set_key("YOUR_TOOLCHEST_KEY")
- 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.
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)
The R client requires the
reticulate
package,
version 1.25 or greater.
Install or update reticulate
with:
install.packages("reticulate")
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.
For more details, see the INSTALL page. If you’re having trouble with installation, consult the page and/or contact Toolchest directly.
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")
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")
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
)