Prerequisites: Python, pip, and Conda

This section describes how to install Python, pip, and Conda if if they are not already installed on your system (or if you are not sure whether they are installed). SEISMIC-RNA does not require that pip and Conda are installed, but we recommend using them because they make installing SEISMIC-RNA and its dependencies much easier, especially for novice users.

Install Conda

Installing Conda installs Python and pip automatically, so it is the easiest option to start. Visit the webpage for installing Conda (https://docs.conda.io/projects/conda/en/latest/user-guide/install/), click the link for your operating system under “Regular installation”, download the installer named “Miniconda installer for …”, and follow the rest of the instructions. You may answer “yes” to all the default options if you so desire. Make sure that you remember the path where conda is being installed. On Linux and macOS, the default is ~/miniconda3.

Initialize Conda

After installing Conda, you will need to initialize it so that it is set up to run properly. Initialize by typing this in the command line, making sure to replace /path/to/your/conda with the actual path in which Conda was installed, plus /condabin/conda (for example, if the installation path were ~/miniconda3, then the path to type would be ~/miniconda3/condabin/conda):

/path/to/your/conda init

If it worked, then you will see a message that looks similar to this:

no change     /home/myname/conda/condabin/conda
no change     /home/myname/conda/bin/conda
no change     /home/myname/conda/bin/conda-env
no change     /home/myname/conda/bin/activate
no change     /home/myname/conda/bin/deactivate
no change     /home/myname/conda/etc/profile.d/conda.sh
no change     /home/myname/conda/etc/fish/conf.d/conda.fish
no change     /home/myname/conda/shell/condabin/Conda.psm1
no change     /home/myname/conda/shell/condabin/conda-hook.ps1
no change     /home/myname/conda/lib/python3.9/site-packages/xontrib/conda.xsh
no change     /home/myname/conda/etc/profile.d/conda.csh
changed       /home/myname/.bash_profile

Then, close and reopen your command line (the changes will not take effect until you restart the command line).

Check your installation

Verify that Conda is initialized by typing the following after you have restarted the command line:

which conda

If Conda is initialized, then this command will print either the path to the Conda executable, such as this:

/home/myname/miniconda3/condabin/conda

or a several lines of code that look like this:

conda () {
    \local cmd="${1-__missing__}"
    case "$cmd" in
        (activate | deactivate) __conda_activate "$@" ;;
        (install | update | upgrade | remove | uninstall) __conda_exe "$@" || \return
            __conda_reactivate ;;
        (*) __conda_exe "$@" ;;
    esac
}

If it is not initialized, then you will get an error message that says Conda was not found.

Troubleshooting Conda installation/initialization

If you encounter any errors, refer to the Conda documentation at https://docs.conda.io/projects/conda/en/latest/user-guide/troubleshooting.html.