Installation

Conda/Bioconda¶

Strobealign is available from Bioconda. Follow the Bioconda setup instructions. Then

conda create -n strobealign strobealign samtools  # install strobealign
conda activate strobealign                        # activate environment
strobealign --version                             # test the installation

You can also use other Conda-compatible package managers such as pixi or Mamba.

Homebrew¶

Strobealign is available in Homebrew core:

brew install strobealign

Cargo¶

Strobealign is available as a crate on crates.io.

To install it, you need a recent Rust version, which you can get via Rustup (the Rust packaged with Debian and Ubuntu is usually too old). This will give you the cargo command.

RUSTFLAGS='-C target-cpu=native' cargo install --locked strobealign

From source¶

This will allow you to install the in-development version of strobealign.

You need to have Rust installed; see the previous section.

git clone https://github.com/ksahlin/strobealign
cd strobealign
RUSTFLAGS='-C target-cpu=native' cargo build --release

The binary is then available at target/release/strobealign.

Python bindings¶

Experimental Python bindings were available in the C++ version of strobealign (until version 0.17.0) and have not been ported to Rust. We may add them back, but until then, you will need to get strobealign 0.17.0, and can then install them with pip install .. The only documentation for the moment are the tests in tests/*.py.