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CLI Conda Installation

SEGUL CLI is available on Bioconda. To install SEGUL CLI, make sure you have Conda installed on your system and Bioconda channel is added to your Conda configuration. Then, you can install SEGUL CLI by running the following command:

conda install bioconda::segul

Or if you use mamba:

mamba install segul

Supported Platforms​

  • Linux (ARM64, x86_64, required GLIBC 2.17+)
  • macOS (Intel and Apple Silicon)
tip

SEGUL Conda installation depends on libgcc-ng version 12 or higher. If you encounter libgcc-ng incompatibility issues, often found in old Linux distributions, you can try updating libgcc-ng using the following command:

conda install conda-forge::libgcc-ng

Then, try to install SEGUL CLI again. Alternatively, on Linux, you can install the Linux MUSL binary. For better compatibility on any operating system, you can also try to install using the package manager.

Detailed Installation Guide​

Install Miniforge​

If you start fresh, we recommend using Miniforge. First, download the Miniforge installer from the Miniforge GitHub release page. The README file in the Miniforge also contains a quick link to the latest release.

Briefly, you can download the installer using wget:

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

Or using curl:

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

After downloading the installer, install Miniforge by running the following command:

bash Miniforge3-$(uname)-$(uname -m).sh

Detailed installation instructions for Miniforge can be found here.

Check Conda and Mamba Installation​

You can check both by checking the Mamba version:

mamba --version

It will print the Mamba and Conda versions if installed correctly.

For example:

mamba 1.5.8
conda 24.5.0

Add Bioconda Channel​

Next, you need to add the Bioconda channel to your Conda configuration:

conda config --add channels bioconda

Install SEGUL CLI​

Finally, you can install SEGUL CLI using the following command:

mamba install segul

To test the SEGUL CLI installation​

To check the version number:

segul --version

To print the help message on your terminal:

segul