Editing Nanopore RNA Sequencing Protocol (section)

====Conda====

Most of the rest of the software (like '''samtools''') is more easily installed using '''Conda''' rather than directly from GitHub. Therefore, before we do anything else, we’re going to make sure Conda is installed on our workstation computer. If you suspect Conda is already installed on the system, run the conda <code>-V</code> command in the shell to see if it returns anything. You could, in theory, install all of the required software without ''Conda'', but I '''highly discourage''' it due to how much we will need to install and how simplified this process is using ''Conda''.

To install, first go to the [https://docs.conda.io/en/latest/miniconda.html Miniconda documentation page] and download the shell script appropriate for your system (note the ''Python'' version requirements). Then, drop the script in your user root folder and execute the following commands in ''Terminal'' (in sequential order):

{{note|Make sure you are in your root folder and you edit the name of the shell script below to match yours before executing the bash command below! Additionally, if you do not know how to access ''Terminal'', on Linux it can be pulled up with the keys <code>ctrl</code> + <code>alt</code> + <code>T</code> pressed simultaneously.}}

<code>Bash</code>
<syntaxhighlight lang="Bash">
bash Miniconda3-py39_4.12.0-Linux-x86_64.sh

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
</syntaxhighlight>

In case you an unfamiliar with it, ''Terminal'' is an application on both ''Linux'' and ''Mac'' machines that gives you access to the shell. On Linux, it can be pulled up if you press the keys <code>ctrl</code> + <code>alt</code> + <code>T</code> simultaneously. You can run commands in here, which is usually for editing and moving files, changing permissions, installing software, or executing scripts.

Now you can install software via ''Conda'' using the <code>conda install</code> command in ''Terminal''.