Installation

salmon 2.0 is a single self-contained binary. Pick whichever method fits your environment.

The release install script downloads the right prebuilt binary for your OS/architecture and puts it on your PATH:

curl --proto '=https' --tlsv1.2 -LsSf \
  https://github.com/COMBINE-lab/salmon/releases/latest/download/salmon-cli-installer.sh | sh

Prebuilt binaries are provided for Linux and macOS on both x86-64 and aarch64. The x86-64 build targets a broad SIMD floor (SSE4.2-era) and selects AVX2 at runtime where available, so one binary runs on essentially any modern CPU.

If you have a Rust toolchain (≥ 1.91):

cargo install salmon-cli

This builds and installs the salmon binary from crates.io.

conda install -c bioconda -c conda-forge salmon

The salmon package tracks the 2.0 (Rust) line. The final C++ release remains available as salmon-cpp for reproducibility.

docker run --rm -v "$PWD:/data" -w /data \
  combinelab/salmon:latest salmon --version

git clone https://github.com/COMBINE-lab/salmon
cd salmon
cargo build --release
# binary at target/release/salmon

The repository ships a .cargo/config.toml that pins the portable SIMD floor; release builds use it automatically.

Verify

salmon --version
salmon --help