Installation

Pre-compiled binaries

Pre-built binaries are available from the GitHub Releases page for Linux and macOS.

curl -fsSL https://github.com/seqeralabs/RustQC/releases/latest/download/rustqc-linux-x86_64.tar.gz | tar xz --strip-components=1
chmod +x ./rustqc
sudo mv ./rustqc /usr/local/bin/
rustqc --version

SIMD-optimized builds are also available for faster performance on modern CPUs. Replace the download URL above with one of:

AVX2 (x86-64-v3) — recommended for most modern servers (Haswell/Zen 1+, 2013+): rustqc-linux-x86_64-v3.tar.gz
AVX-512 (x86-64-v4) — fastest, requires Skylake-X/Zen 4+ (2017+): rustqc-linux-x86_64-v4.tar.gz

Run rustqc --version to see which features your CPU supports and whether a faster build is available.

curl -fsSL https://github.com/seqeralabs/RustQC/releases/latest/download/rustqc-linux-aarch64.tar.gz | tar xz --strip-components=1
chmod +x ./rustqc
sudo mv ./rustqc /usr/local/bin/
rustqc --version

An SVE-optimized build is also available for AWS Graviton 3+, Google Axion, and NVIDIA Grace instances. Replace the download URL above with:

SVE (neoverse-v1) — 256-bit vectors vs NEON’s 128-bit baseline: rustqc-linux-aarch64-neoverse-v1.tar.gz

curl -fsSL https://github.com/seqeralabs/RustQC/releases/latest/download/rustqc-macos-aarch64.tar.gz | tar xz --strip-components=1
chmod +x ./rustqc
sudo mv ./rustqc /usr/local/bin/
rustqc --version

An M1-optimized build with better scheduling for Apple Silicon is also available. Replace the download URL above with:

Apple M1 — optimized for M-series chips (M1/M2/M3/M4, backward compatible): rustqc-macos-aarch64-apple-m1.tar.gz

curl -fsSL https://github.com/seqeralabs/RustQC/releases/latest/download/rustqc-macos-x86_64.tar.gz | tar xz --strip-components=1
chmod +x ./rustqc
sudo mv ./rustqc /usr/local/bin/
rustqc --version

Docker

Run RustQC without any local installation using Docker:

# Run all RNA-seq QC analyses in a single pass
docker run -v $(pwd):/data ghcr.io/seqeralabs/rustqc:latest \
  rustqc rna /data/sample.bam --gtf /data/genes.gtf -p -o /data/output/

SIMD-optimized Docker images are also available for better performance on capable hardware:

# x86_64 with AVX2 (recommended for most modern x86 servers)
docker run -v $(pwd):/data ghcr.io/seqeralabs/rustqc:latest-avx2 \
  rustqc rna /data/sample.bam --gtf /data/genes.gtf -p -o /data/output/

# x86_64 with AVX-512 (Skylake-X, Zen 4+)
docker run -v $(pwd):/data ghcr.io/seqeralabs/rustqc:latest-avx512 \
  rustqc rna /data/sample.bam --gtf /data/genes.gtf -p -o /data/output/

# aarch64 with SVE (Graviton 3+, Axion, Grace)
docker run -v $(pwd):/data ghcr.io/seqeralabs/rustqc:latest-sve \
  rustqc rna /data/sample.bam --gtf /data/genes.gtf -p -o /data/output/

Build from source

Building from source requires the Rust toolchain, a C++ compiler, and a few system libraries needed by rust-htslib for SAM/BAM/CRAM I/O. The C++ compiler is used both by rust-htslib and by RustQC’s preseq FFI shim (a small C++ wrapper that links against the host’s std::mt19937 and std::binomial_distribution for exact bootstrap compatibility with upstream preseq).

Install from crates.io

If you already have the Rust toolchain and system dependencies installed, you can install directly from crates.io:

cargo install rustqc

Build from a git clone

Select your operating system for build instructions:

# Install system dependencies
brew install cmake zlib bzip2 xz curl openssl

# Install Rust (if not already installed)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

# Build RustQC
git clone https://github.com/seqeralabs/RustQC.git
cd RustQC
cargo build --release

# Binary is at target/release/rustqc
./target/release/rustqc --version

# Install system dependencies
sudo apt install cmake zlib1g-dev libbz2-dev liblzma-dev \
  libcurl4-openssl-dev libssl-dev clang

# Install Rust (if not already installed)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

# Build RustQC
git clone https://github.com/seqeralabs/RustQC.git
cd RustQC
cargo build --release
./target/release/rustqc --version

# Install system dependencies
sudo dnf install cmake zlib-devel bzip2-devel xz-devel \
  libcurl-devel openssl-devel clang

# Install Rust (if not already installed)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

# Build RustQC
git clone https://github.com/seqeralabs/RustQC.git
cd RustQC
cargo build --release
./target/release/rustqc --version

The compiled binary is at target/release/rustqc. You can copy it to a directory on your PATH for convenient access. Release builds use link-time optimization (LTO) and symbol stripping for better performance and a smaller binary.

The system dependencies are: cmake, zlib, bz2, lzma, curl, ssl, and a C++ compiler (clang or g++).

Extra performance

Pre-built SIMD-optimized binaries are available (see tabs above) that already leverage AVX2, AVX-512, or SVE. If you’re building from source and want to target your exact CPU, you can squeeze out additional performance:

RUSTFLAGS="-C target-cpu=native" cargo build --release

For a further 5–20% speedup on a machine you run RustQC on regularly, you can use Profile-Guided Optimization (PGO). This lets the compiler optimize hot code paths based on a real workload:

# 1. Build an instrumented binary
RUSTFLAGS="-Cprofile-generate=/tmp/pgo-data" cargo build --release

# 2. Run it on a representative BAM file
./target/release/rustqc rna your_sample.bam --gtf genes.gtf -p -o /tmp/pgo-out

# 3. Merge the profile data
llvm-profdata merge -o /tmp/pgo-data/merged.profdata /tmp/pgo-data

# 4. Rebuild using the profile
RUSTFLAGS="-Cprofile-use=/tmp/pgo-data/merged.profdata -C target-cpu=native" \
  cargo build --release

Verify installation

rustqc --version
rustqc --help

If the binary is not on your PATH, use the full path to the compiled binary:

./target/release/rustqc --version
./target/release/rustqc --help