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 23.10 but should also work on other recent versions of Ubuntu, including the latest LTS release as of this writing, Ubuntu 22.04.

Installing dependencies via APT

We will install some dependencies using Ubuntu's default package manager, APT.

First, update the package lists.

sudo apt update

Then, install the first set of packages. The table below describes what we will install.

Software	Description
Git	Version control system used by RNA-clique (usually installed by default)
wget	Command-line utility for downloading files from the web (usually installed by default)
NCBI BLAST+	Popular implementation of the BLAST local sequence alignment algorithm
build-essential	Metapackage containing tools useful for building software , including Perl modules
cpanminus	Package manager for Perl

sudo apt install git wget ncbi-blast+ ncbi-blast+ ncbi-blast+-legacy \
                 build-essential cpanminus

BioPerl can also be installed via APT. The package and its dependencies include many recommendations that we don't need—you can specify --no-install-recommends to avoid installing those.

sudo apt install bioperl --no-install-recommends

Installing GNU Parallel (optional)

Some parts of RNA-clique can use GNU Parallel to run multiple jobs simultaneously. Parallelization can speed up these parts on systems with more than one logical core ("thread"). GNU parallel be installed via APT.

sudo apt install parallel

Installing Array::Heap

We will use cpanmius to install the Array::Heap Perl module, since it isn't available in Ubuntu's default software repositories.

sudo cpanm Array::Heap

Installing Miniconda

The conda package and environment manager will be useful for setting up the Python dependencies of RNA-clique. If you already have a conda installation, you can skip to the next step, Installing the rna-clique conda environment First, download the Miniconda installer:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Then, run the installer.

bash Miniconda3-latest-Linux-x86_64.sh

Unless you have a reason to install somewhere else, you can install to the default locaton Miniconda suggests.

When asked about initializing Miniconda for the current shell, say yes.

When the installation has finished, you will need to restart your shell.

Downloading RNA-clique

For now, you can download RNA-clique by cloning its GitHub repository.

git clone --recurse-submodules https://github.com/actapia/rna_clique

Installing the rna-clique conda environment

Make sure you are in the rna_clique repository that you cloned with git.

cd rna_clique

Then, create a conda environment from the environment.yml file in the root of the repository.

conda env create -f environment.yml --name rna-clique

When asked to confirm that you want to install the dependencies, say yes.

When creation of the new environment has finished, you can activate the environment to ensure you are running Python with the needed dependencies:

conda activate rna-clique