Bioconda (stable 1.x release)

Bioconda currently provides SeqFu 1.x, the stable release, not the 2.0.0-alpha development version documented on this website. For the corresponding commands and options, use the stable version documentation.

The recommended installation method is via Bioconda, supported on both Linux and macOS. It installs the full set of tools: the seqfu binary, all the fu-* utilities and the helper scripts.

conda install -c conda-forge -c bioconda "seqfu>=1.30"

A dedicated environment keeps things tidy:

conda create -n seqfu -c conda-forge -c bioconda seqfu
conda activate seqfu

Ask for a recent version explicitly: 0.x releases are very old and no longer supported.

Pre-compiled binaries (development version)

Pre-compiled binaries are attached to each release. Starting with v1.29.0, releases include the main seqfu binary for Linux and macOS, on both x86_64 and ARM64/aarch64. The binaries contain the core tools only; install from Bioconda to get the utilities too.

To install the latest matching binary into $HOME/.local/bin:

curl -fsSL https://telatin.github.io/seqfu2/install.sh | sh

The installer detects the latest release and your platform, downloads the matching asset, verifies it against the SHA-256 digest reported by GitHub, installs it as seqfu and marks it executable. Set SEQFU_INSTALL_DIR to choose another destination:

curl -fsSL https://telatin.github.io/seqfu2/install.sh | SEQFU_INSTALL_DIR=/opt/bin sh

Build from source

SeqFu is written in Nim and requires Nim 2.2 or newer.

1. Install Nim (instructions); choosenim is the easiest option where available.

2. Clone the repository and build:

   git clone https://github.com/telatin/seqfu2
   cd seqfu2
   make
   

3. The binaries are written to ./bin. Run the test suite with make test.

nimble build also works, and downloads the required Nim packages.

It is possible to compile SeqFu on Windows, but the platform is not supported.