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-0.11.11.tar.gz
(61.1 kB
view hashes)
Built Distribution
Close
Hashes for toolchest_client-0.11.11-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 21d0385ee8eb348a444ed1df208916e7695dd7f4b4579c45bce139d215cd4084 |
|
MD5 | 82edddfb903acc4ed192c95600367158 |
|
BLAKE2b-256 | 4307809406fccbd0df0610ef24248d618af7c09cc64444e0f45f84537e543120 |