finch-rs
A genomic minhashing implementation in Rust
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Download Latest Version (.zip)- ci.yml
- release.yml
- cli.rs
- main.rs
- query.fa
- refs.fa
- test_cli.rs
- Cargo.toml
- finch.capnp
- finch_capnp.rs
- json.rs
- mash.capnp
- mash.rs
- mash_capnp.rs
- mod.rs
- counts.rs
- hashing.rs
- mash.rs
- mod.rs
- scaled.rs
- distance.rs
- errors.rs
- filtering.rs
- lib.rs
- python.rs
- statistics.rs
- Cargo.toml
- codemeta.json
- depth_distance.png
- generate_figures.ipy
- paper.bib
- paper.md
- .dockerignore
- .gitignore
- Cargo.lock
- Cargo.toml
- clippy.toml
- CODE_OF_CONDUCT.md
- Dockerfile
- LICENSE.txt
- pyproject.toml
- README.md
- test_python.py
# Installation Guide
1. Get the code
git clone https://github.com/onecodex/finch-rs
Downloads the entire project code from GitHub to your computer.
cd finch-rs
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install finch-sketch
Installs the package published on PyPI directly โ no need to clone the source.
pip install maturin
Installs the package published on PyPI directly โ no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Docker
EasyPrerequisites
- Git Needed to download the project code from GitHub.
- Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin:main build --features=python --release --strip --interpreter=python3.10 --compatibility=manylinux2010
Runs the built image as an actual container.
Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.
Pulled directly from this repo's README.
4. Python
EasyPrerequisites
pip install finch-sketch
Installs the package published on PyPI directly โ no need to clone the source.
pip install maturin
Installs the package published on PyPI directly โ no need to clone the source.
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
5. Rust
MediumPrerequisites
- Git Needed to download the project code from GitHub.
- Rust (rustup) Installing via rustup also installs cargo.
cargo build --release
Compiles the Rust project.
cargo run
Builds and then immediately runs the program.
If cargo build finishes without errors, it worked. The executable is created under target/.
// repository documentation
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