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RustQC

Installation

Pre-compiled binaries

Section titled “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-macos-aarch64.tar.gz | tar xz --strip-components=1
chmod +x ./rustqc
sudo mv ./rustqc /usr/local/bin/
rustqc --version

Docker

Section titled “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/

Build from source

Section titled “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

Section titled “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

Section titled “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

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

Section titled “Extra performance”

When building from source you can squeeze out additional performance by targeting your specific CPU architecture. This enables use of SIMD instructions (AVX2, etc.) that the pre-built binaries cannot use because they target a generic baseline:

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

Section titled “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