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.
Release files for toolchest-client 0.11.14
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| toolchest_client-0.11.14.tar.gz | 61.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| toolchest_client-0.11.14-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 146.8 kB
Release files / toolchest_client-0.11.14.tar.gz
| Download URL | toolchest_client-0.11.14.tar.gz |
|---|---|
| Size | 61.4 kB |
| Tags | Source |
|
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No |
| Uploaded via |
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|
Release files / toolchest_client-0.11.14-py3-none-any.whl
| Download URL | toolchest_client-0.11.14-py3-none-any.whl |
|---|---|
| Size | 85.4 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
poetry/1.3.1 CPython/3.8.16 Linux/5.15.0-1030-aws
|
