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 Sequoia 15.0.1 and has been tested so far on Intel Macs only. The guide may also work on Apple Silicon, but the developer of this software has not yet been able to test the guide on such a machine. Additionally, the guide should also work on other recent versions of macOS, but such configurations are untested.
Installing command line developer tools
Installation requires some commands (e.g., git) that are part of the macOS
command line developer tools, which are not installed by default. To install
them, run the following in the Terminal.
If the command line developer tools have not been installed already, you should see a graphical dialog prompting you to confirm installation. Click "Install" and agree to the license agreement to begin installation .Wait for the install to complete before continuing.
Download RNA-clique
For now, you can download RNA-clique by cloning its GitHub repository.
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.
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.
Installing Bash
We will install a few packages using Homebrew.
First, we will install Bash, which is a Unix shell. The version of Bash that comes installed on macOS is very out of date, but RNA-clique requires some new features of Bash.
Second, we will install NCBI BLAST+, a popular implementation of the BLAST local sequence alignment software.
Third, we will install cpanminus`, a Perl package manager that will help us install the Perl dependencies.
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 brew.
Installing Bio::SeqIO
We can use cpan to install the Bio::SeqIO Perl module.
macOS may ask you to permit Terminal to access certain files and settings on your computer. You can safely allow Terminal that access.
Installing Array::Heap
Again, we can use cpan.
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:
Then, run the installer.
Agree to the license terms. Unless you have a reason to install somewhere else, you can install to the default location 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.
Installing the rna-clique conda environment
Make sure you are in the rna_clique repository that you cloned with git.
Then, create a conda environment from the environment.yml file in the root
of the repository.
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: