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Installation

Supported platforms

bsbit supports 64-bit Linux on x86-64 (Intel or AMD), either natively or under WSL2, and on AArch64 (ARM64) with NEON.

Install from Bioconda

Coming soon

Bioconda installation is coming soon. It will be the recommended installation method, especially on shared systems and HPC clusters.

Install from source

Requirements

The following tools and libraries are required to build bsbit and run the documented workflow:

  • Rust 1.89 or later
  • A C/C++ toolchain with OpenMP support
  • Autoconf, Automake, Libtool, Make, pkg-config, Git, and curl
  • Development libraries for zlib, bzip2, liblzma, and libdeflate
  • samtools and tabix

Choose one of the following ways to prepare a complete build environment.

Using Conda or Mamba

Conda can provide the compilers, Rust toolchain, native libraries, and workflow tools in an isolated user-space environment:

conda create -n bsenv -c conda-forge -c bioconda \
  'rust>=1.89' c-compiler cxx-compiler make \
  autoconf automake libtool pkg-config git curl \
  zlib bzip2 xz libdeflate samtools htslib
conda activate bsenv

mamba can be used in place of conda. Activate bsenv again before building or running bsbit in a new shell.

Using system tools

On Ubuntu or WSL2, install the native dependencies and workflow tools with APT:

sudo apt-get update
sudo apt-get install --yes \
  build-essential autoconf automake libtool pkg-config curl git \
  zlib1g-dev libbz2-dev liblzma-dev libdeflate-dev \
  samtools tabix

If cargo is unavailable, install Rust with rustup:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
. "$HOME/.cargo/env"
rustup default stable

Build and install bsbit

Clone the pinned native dependencies and install the complete CLI using either the Conda or system environment:

git clone --recurse-submodules https://github.com/wbvguo/bsbit.git
cd bsbit
cargo install --locked --path crates/bsbit-cli \
  --root "${CONDA_PREFIX:-$HOME/.cargo}"

After installation, the bsbit executable should be available on PATH.

Verify the installation

Confirm that the CLI is available and inspect the installed version and commands:

bsbit --version
bsbit --help
Verify runtime compatibility

CPU features visible inside WSL2, VMs, containers, and cluster jobs can differ from those available on the host. Check the environment where bsbit will actually run:

bsbit cpu

The command reports the detected features and selected backend. See the bsbit cpu reference for details.

Next: Use the quick start for common commands, or review the sequencing data support.