Installing RNA-clique for macOS

This guide will walk you through installing RNA-clique on macOS. Since RNA-clique currently has no graphical interface, basic command-line skills are needed for both installation and use of the software.

This guide is designed for macOS 26 Tahoe and has also been tested on macOS 15 Sequoia via GitHub Actions runners. Newer versions of macOS will likely work, but older versions probably will not.

Installing Homebrew

Homebrew (brew) is a package manager for macOS---it allows the user to install and update software packages via the command line. We will use brew to install some of the dependencies of RNA-clique, but we need to install the package manager itself first.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

You will most likely need to enter your password to install Homebrew as root. The install script will also ask you to confirm that you want to install the needed software.

After the install has finished, run the commands that the installer suggests to add Homebrew to your PATH, and the restart your shell.

Installing BLAST and Python

We will use brew to install NCBI BLAST+, a popular implementation of the BLAST local sequence alignment software.

We will also install a new version of Python since macOS comes pre-installed with a version that is too old to work with RNA-clique.

brew install blast python@3.14

Creating a virutal environment

It is good practice to install our software to a separate Python virtual environment. Software installed in the virtual environment will only be usable when we have the virtual environment "activated," so it won't clutter or conflict with the other software installed on the system.

python3.14 -m venv rna_clique_env

Then, activate the environment with the virtual environment's activate script.

. rna_clique_env/bin/activate

You should see that (rna_clique_env) appears at the beginning of your prompt, letting you know.

Installing RNA-clique

You can install RNA-clique from the Python Package Index using pip. Alternatively, you can build the package yourself from the Git repository.

python -m pip install rna-clique

Note

When you log out and log back into your shell, you will need to reactivate the virtual environment using the activate script.