2 releases
0.0.15 | Jul 31, 2024 |
---|---|
0.0.14 | Jun 11, 2024 |
#151 in Machine learning
117 downloads per month
105KB
2K
SLoC
gtars
is a rust crate that provides a set of tools for working with genomic interval data. Its primary goal is to provide processors for our python package, geniml
, a library for machine learning on genomic intervals. However, it can be used as a standalone library for working with genomic intervals as well.
gtars
provides three things:
- A rust library crate.
- A command-line interface, written in rust.
- A Python package that provides bindings to the rust library.
Repository organization (for developers)
This repo is organized like so:
- A rust library crate (
/gtars/lib.rs
) that provides functions, traits, and structs for working with genomic interval data. - A rust binary crate (in
/gtars/main.rs
), a small, wrapper command-line interface for the library crate. - A rust crate (in
/bindings
) that provides Python bindings, and a resulting Python package, so that it can be used within Python.
This repository is a work in progress, and still in early development.
Installation
To install gtars
, you must have the rust toolchain installed. You can install it by following the instructions here.
You may build the binary locally using cargo build --release
. This will create a binary in target/release/gtars
. You can then add this to your path, or run it directly.
Usage
gtars
is very early in development, and as such, it does not have a lot of functionality yet. However, it does have a few useful tools. To see the available tools, run gtars --help
. To see the help for a specific tool, run gtars <tool> --help
.
Alternatively, you can link gtars
as a library in your rust project. To do so, add the following to your Cargo.toml
file:
[dependencies]
gtars = { git = "https://github.com/databio/gtars" }
Testing
To run the tests, run cargo test
.
Contributing
New internal library crate tools
If you'd like to add a new tool, you can do so by creating a new module within the src folder.
New public library crate tools
If you want this to be available to users of gtars
, you can add it to the gtars
library crate as well. To do so, add the following to src/lib.rs
:
pub mod <tool_name>;
New binary crate tools
Finally, if you want to have command-line functionality, you can add it to the gtars
binary crate. This requires two steps:
- Create a new
cli
usingclap
inside theinterfaces
module ofsrc/cli.rs
:
pub fn make_new_tool_cli() -> Command {
}
- Write your logic in a wrapper function. This will live inside the
functions
module ofsrc/cli.rs
:
// top of file:
use tool_name::{ ... }
// inside the module:
pub fn new_tool_wrapper() -> Result<(), Box<dyn Error>> {
// your logic here
}
Please make sure you update the changelog and bump the version number in Cargo.toml
when you add a new tool.
VSCode users
If you are using VSCode, make sure you link to the Cargo.toml
inside the .vscode
folder, so that rust-analyzer
can link it all together:
{
"rust-analyzer.linkedProjects": [
"./vocab/Cargo.toml",
"./Cargo.toml"
"./new-tool/Cargo.toml"
]
}
Dependencies
~2–3MB
~55K SLoC