Toolchest Python Client

Toolchest provides APIs for scientific and bioinformatic data analysis. It allows you to abstract away the costliness of running tools on your own resources by running the same jobs on secure, powerful remote servers.

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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.