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seqprocseqprocseqproc

Installation

Requirements

Section titled “Requirements”

The current source tree requires:

  • a Rust toolchain at version 1.88 or newer;
  • Git;
  • a C toolchain and the usual system build tools used by Rust dependencies.

Install a release

Section titled “Install a release”

Checksummed archives for supported platforms and a shell installer are published on the GitHub Releases page. The corresponding crates.io installation is:

Terminal window
cargo install --locked seqproc

Build the pinned source tree

Section titled “Build the pinned source tree”

Clone the repository and build with its committed lockfile:

Terminal window
git clone https://github.com/COMBINE-lab/seqproc.git
cd seqproc
cargo build --release --locked
./target/release/seqproc --version --verbose

Using --locked prevents Cargo from silently selecting dependency versions other than those recorded in Cargo.lock.

The repository configuration uses target-cpu=native, so a local source build is optimized for—and should be run on—the host that compiled it. Do not redistribute that executable as a generic binary.

Tagged artifacts instead use fixed, reviewable CPU targets:

  • x86_64 Linux and macOS: x86-64-v3, including AVX2;
  • aarch64 Linux: Neoverse N1;
  • aarch64 macOS: Apple A14.

The x86_64 executable makes a best-effort check of the complete v3 feature set through raw CPUID before processing and reports an actionable incompatibility. seqproc --version --verbose reports the compiler, target, target features, CPU floor, and compiled ANTISEQUENCE SIMD backend.

ANTISEQUENCE itself keeps an SSE2/NEON library default. For a seqproc compatibility control or a pre-AVX2 x86_64 host, build its baseline backend and override the repository’s native code-generation setting:

Terminal window
RUSTFLAGS="" cargo build --release --locked --no-default-features \
  --features antisequence/baseline-simd

To put the local build on your path:

Terminal window
install -Dm755 target/release/seqproc "$HOME/.local/bin/seqproc"

Make sure $HOME/.local/bin is present in PATH, or invoke the binary by its full path.

Optional allocator builds

Section titled “Optional allocator builds”

For controlled performance experiments, allocator features are forwarded to the ANTISEQUENCE backend:

Terminal window
cargo build --release --locked --features mimalloc
# or
cargo build --release --locked --features jemalloc

Use the default build unless you are benchmarking allocator behavior. Record the selected feature, compiler, target, and commit whenever results will be compared.

Confirm the installation

Section titled “Confirm the installation”
Terminal window
seqproc --help
seqproc --version --verbose
seqproc run --help

You should see the run, validate, and explain commands. Continue with the quick start.