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.
The Toolchest client is available on PyPI:
pip install toolchest-client
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.
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.