Rosella

Install

Conda

conda create -n rosella -c bioconda rosella
conda activate rosella
rosella --version

Cargo

With Rust 1.88 or later and a C compiler, from crates.io or straight from GitHub:

cargo install --locked rosella
cargo install --locked --git https://github.com/rhysnewell/rosella

Read mapping, gene calling and the marker search are built in, so nothing else is needed.

macOS binary

Each release ships a binary for arm64 macOS. Put it on your PATH:

install -m 755 rosella /usr/local/bin/
rosella --version

GPU

On macOS --gpu runs on Metal. Metal ships with macOS. On Linux --gpu runs on CUDA. It needs the NVIDIA driver plus cuBLAS and NVRTC from CUDA 12. Conda can install the two libraries:

conda create -n cuda -c conda-forge "cuda-version=12" libcublas cuda-nvrtc
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH

When no GPU can be opened, --gpu logs a warning and the run goes on the CPU.

Examples

Map each sample’s reads and keep their depth in one directory. --interleaved takes interleaved reads, and -b takes BAMs…