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💿 Installing gtars

gtars is available in many forms to support your chosen compute environment and framework. We've extended our core rust implementation into many forms:

  • Rust Library: The core rust implementation can be used as a library in other Rust projects, allowing for deep integration and customization.
  • Command Line Interface (CLI): The core rust implementation can be installed via cargo. This is the most flexible way to use gtars, and is suitable for any environment that supports rust.
  • Python Package: A Python package is available via pip, making it easy to integrate gtars into Python-based workflows and applications.
  • Wasm/JS Package: A WebAssembly (Wasm) package is available for JavaScript environments, allowing gtars to be used in web applications and other JS-based projects.
  • R bindings (package): R bindings are available for R users, enabling the use of gtars within R scripts and applications.

Each environment has its own installation instructions, which are detailed below.

Rust Library

To use gtars as a Rust library, add the following to your Cargo.toml. We feature-gate optional dependencies to keep the base install small.

[dependencies]
gtars = { version = "0.5.0", features = ["uniwig", "tokenizers"] }

Then, in your Rust code, you can import and use gtars as follows:

use gtars::uniwig;
// Your code here

For more details, refer to the gtars Rust documentation.

Command Line Interface (CLI)

To install the gtars CLI, you need to have Rust and Cargo installed. You can then install gtars using the following command: 

cargo install gtars-cli

Similarly, we feature-gate binary dependencies maximize compatibility and minimize install size. You can specify features during installation like so:

cargo install gtars-cli --features "uniwig tokenizers"

Additionally, you can add all features with: 

cargo install gtars-cli --all-features
Once installed, you can verify the installation by running:

gtars --help

Python Package

To install the gtars Python package, you can use pip. The package is available on PyPI and can be installed with the following command: 

pip install gtars

You can then import and use gtars in your Python code as follows:

from gtars.tokenizers import Tokenizer

tokenizer = Tokenizer.from_pretrained("databio/atacformer-base-hg38")

Wasm/JS Package

To use gtars in a JavaScript environment, you can install the Wasm package via npm. First, ensure you have Node.js and npm installed. Then, you can install the gtars package with the following command: 

npm install @databio/gtars-js

You can then import and use gtars in your JavaScript code as follows:

import { Overlapper } from '@databio/gtars-js';

const universe = [
    ['chr1', 100, 200],
    ['chr1', 150, 250],
    ['chr2', 300, 400],
]

const overlapper = new Overlapper(universe, 'ailist');
console.log(`Using backend: ${overlapper.get_backend()}`);

const query = ['chr1', 180, 220];
const overlaps = overlapper.find(query);

console.log(`Overlaps for ${query}:`, overlaps);

R Package

COMING SOON.