Installing RNA-clique for Ubuntu

This guide will walk you through installing RNA-clique on Ubuntu. The guide assumes you have some basic familiarity working with Ubuntu using the command line. The guide is designed for Ubuntu 26.04 and has also been tested on Ubuntu 24.04 via GitHub Actions runners.

Installing dependencies via APT

RNA-clique requires that NCBI BLAST+, a popular implementation of the BLAST sequence alignment algorithm, be installed.

For Python, we also need to be able to create virtual environments, so we will need to install venv. Some Python packages we will install also need to be built using a C++ compiler, so we will install the common g++ compiler and the Python development headers. We can install all of these using Ubuntu's default package manager, APT.

First, update the package lists.

sudo apt update

Then, install NCBI BLAST+ and g++.

sudo apt install ncbi-blast+ ncbi-blast+-legacy g++ python3-venv libpython3-dev

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 -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.