Python client for Toolchest
Project description
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
toolchest_client-0.11.5.tar.gz
(62.7 kB
view hashes)
Built Distribution
Close
Hashes for toolchest_client-0.11.5-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 52df0b537e83f785e7518f15fbab7f91092158dfffd6d1a5c5af0e8c1515c5c4 |
|
MD5 | 5e2c2c85461c53f34c62c74be30757b7 |
|
BLAKE2b-256 | 8f0d6512c96008276dc96dcfe429c8fafcb85afe9dceb3c3cc34f31c5edc4ab1 |