CLI Installation

The SEGUL CLI is a single executable named segul. Pick the method that fits your system:

Method	Platforms	Best for
Installer script	Linux, macOS	The quickest install, no root access needed
Pre-compiled binary	Linux, macOS, Windows, WSL	Manual installs, Windows, offline machines
Conda	Linux, macOS	Conda users and shared environments
Cargo	Any platform Rust supports	Rust users; builds tuned for your hardware
Source code	Any platform Rust supports	The latest code, or beta features

After installing, check that segul runs from any folder:

segul --version

Installer script

On Linux and macOS, run:

curl -fsSL https://segul.app/install.sh | sh

The script picks the right binary for your system and installs it to ~/.local/bin without root access. It tells you if that folder is not on your PATH. On Linux x86_64, it uses the static musl build when your GLIBC is older than 2.34, which is common on HPC clusters.

Pass options after sh -s --, for example curl -fsSL https://segul.app/install.sh | sh -s -- --dir ~/bin.

Option	Description
--dir <path>	Install into another folder, such as --dir ~/bin.
--version <tag>	Install a specific release, such as --version v0.23.2.
--musl	Use the static Linux build even when GLIBC is new enough.
--uninstall	Remove the installed binary. Add --dir if you used a custom folder.

Pre-compiled binary

Download the archive for your system from the latest release:

Linux

• x86_64Modern distributions and WSL↓
• x86_64 staticOlder GLIBC, common on HPC↓
• ARM64ARM servers and boards↓

macOS

• Apple siliconM-series Macs↓
• IntelIntel Macs↓

Windows

• x86_64Most Windows PCs↓
• ARM64Windows on ARM, Copilot+ PCs↓

Linux and WSL

Linux x86_64 comes in two builds. Check your GLIBC version to choose:

ldd --version

• GLIBC 2.34 or newer: use segul-Linux-x86_64.tar.gz. The compiler optimizes it more, so it is faster.
• Older GLIBC: use the fully static segul-Linux-musl-x86_64.tar.gz. It runs on any Linux, including older HPC systems.
• ARM64: use segul-Linux-arm64.tar.gz, available since 0.21.3. It needs GLIBC 2.34 or newer.

1. Download and extract the archive. Replace the file name with the build you chose.

   curl -LJO https://github.com/hhandika/segul/releases/latest/download/segul-Linux-x86_64.tar.gz
   tar xfvz segul-Linux-x86_64.tar.gz

2. If your shell does not recognize the binary, make it executable. Use chmod a+x instead to allow all users.

   chmod +x segul

3. Move segul to a folder on your PATH, such as ~/bin. If the folder is not on your PATH yet, add it to your shell profile. Run echo $SHELL to see your shell: use ~/.bashrc (or ~/.bash_profile) for bash and ~/.zshrc for zsh.

   mkdir -p ~/bin && mv segul ~/bin/
   echo 'export PATH=$PATH:~/bin' >> ~/.bashrc
   source ~/.bashrc

4. Check the installation with segul --version.

WSL performance

On WSL 2, the default, keep large datasets in the Linux file system. Reading files from the Windows partition is 2–3 times faster on WSL 1. See the Microsoft WSL comparison. Native Windows is faster than either.

macOS

Use segul-macOS-arm64.tar.gz for Apple silicon (M-series) Macs and segul-macOS-x86_64.tar.gz for Intel Macs.

1. Download and extract the archive.

   curl -LJO https://github.com/hhandika/segul/releases/latest/download/segul-macOS-arm64.tar.gz
   tar xfvz segul-macOS-arm64.tar.gz

2. If your shell does not recognize the binary, make it executable.

   chmod +x segul

3. Move segul to a folder on your PATH. macOS uses zsh by default, so add the folder to ~/.zshrc.

   mkdir -p ~/bin && mv segul ~/bin/
   echo 'export PATH=$PATH:~/bin' >> ~/.zshrc
   source ~/.zshrc

4. Check the installation with segul --version.

Tip

If you already keep other single-file tools in a folder on your PATH, put segul there. Many PATH entries slow down terminal startup.

Windows

Use segul-Windows-x86_64.zip for most PCs and segul-Windows-arm64.zip for Windows on ARM, such as Copilot+ PCs. Native Windows is faster than running the Linux build in WSL.

1. Download the zip file, right-click it, and select Extract All….
2. Move segul.exe to a folder you keep for command-line tools, such as C:\Tools.
3. Search for env and open Edit the system environment variables. Select Environment Variables…, pick Path under System variables, and select Edit…. Select New, add your folder, and close each dialog with OK.
4. Open a new terminal and check the installation with segul --version.

Tip

Windows Terminal with PowerShell 7 makes terminal work easier. Windows Terminal comes with Windows 11.

Conda

SEGUL is on Bioconda for Linux (x86_64 and ARM64, GLIBC 2.17+) and macOS (Intel and Apple silicon).

I have conda

With the Bioconda channel set up, install SEGUL with conda or mamba:

conda install bioconda::segul

mamba install segul

Start fresh

1. Download and run the Miniforge installer:

   curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
   bash Miniforge3-$(uname)-$(uname -m).sh

2. Open a new terminal and check that conda and mamba work. It prints both versions.

   mamba --version

3. Add the Bioconda channel:

   conda config --add channels bioconda

4. Install SEGUL and check it:

   mamba install segul
   segul --version

libgcc-ng errors

The conda package needs libgcc-ng 12 or newer, which older Linux systems may lack. Update it with conda install conda-forge::libgcc-ng, then try again. On Linux, the static pre-compiled binary or Cargo also avoid the problem.

Cargo

If you use Rust, Cargo compiles SEGUL for your hardware and makes updates easy. Install the Rust toolchain, check that it works, then install SEGUL:

cargo --version
cargo install segul

If compiling fails with a linker or build tool error, install the C build tools for your system and try again:

Debian and Ubuntu

sudo apt install build-essential

Fedora

sudo dnf groupinstall "Development Tools" "Development Libraries"

openSUSE

sudo zypper install -t pattern devel_basis

Windows

Install the GNU toolchain with rustup, which comes with Rust, and make it the default:

rustup toolchain install stable-x86_64-pc-windows-gnu
rustup default stable-x86_64-pc-windows-gnu

Source code

Building from source also needs the Rust toolchain.

Latest code

Install straight from the main branch on GitHub:

cargo install --git https://github.com/hhandika/segul.git

Or clone and build it yourself. The binary is written to target/release/segul; copy it to a folder on your PATH.

git clone https://github.com/hhandika/segul
cd segul/
cargo build --release

Beta features

New features live in the dev branch until testing finishes, and the documentation marks them as beta. Use them for testing only; they may be unstable.

cargo install --git https://github.com/hhandika/segul.git --branch dev

Tip

If cargo is not found right after installing Rust, open a new terminal, or reload your profile with source ~/.zshrc or source ~/.bashrc. If compiling fails, install the C build tools.