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

Documentation & User Guide

Installation

The Toolchest client is available on PyPI:

pip install toolchest-client

Usage

Using a tool in Toolchest is as simple as:

import toolchest_client as toolchest
toolchest.set_key("YOUR_TOOLCHEST_KEY")
toolchest.kraken2(
  tool_args="",
  inputs="path/to/input.fastq",
  output_path="path/to/output.fastq",
)

For a list of available tools, see the documentation.

Configuration

To use Toolchest, you must have an authentication key stored in the TOOLCHEST_KEY environment variable.

import toolchest_client as toolchest
toolchest.set_key("YOUR_TOOLCHEST_KEY") # or a file path containing the key

Contact Toolchest if:

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