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.
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