Provides APIs for scientific and bioinformatic data analysis
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.
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