Detailed Linux Instructions

[## Miniconda-Installation

1. Download Miniconda

   • Miniconda: Miniconda is a smaller version of Anaconda that includes only Conda and fewer utility packages. It's suitable if you want a minimal installation. You can download it from the Miniconda website: https://docs.conda.io/en/latest/miniconda.html

2. Open the terminal and navigate to your Download directory:

   • On most Linux distributions, you can open a terminal by pressing Ctrl + Alt + T or searching for "Terminal" in the application menu.
   • Use the cd command to navigate to the directory where you downloaded the installer. For example, if you downloaded it to your "Downloads" folder, use the following command:

     cd ~/Downloads
     

3. Run the Installer:

   • For Miniconda, use the following command (replace Miniconda3-latest-Linux-x86_64.sh with the actual filename you downloaded):

     bash Miniconda3-latest-Linux-x86_64.sh
     

4. Follow the Installer Instructions:

   • The installer will prompt you to review the license agreement. Press Enter to continue, and then press Enter again to scroll through the license text. Type yes to accept the license.

5. Choose Installation Location:

   • The installer will prompt you to choose the installation location. The default location is usually fine, but you can specify a different path if needed.

6. Initiate Conda:

   • The installer will ask if you want to initialize Conda. Type yes to have Conda added to your PATH so that you can use it in any terminal window.

7. Close and Reopen the Terminal:

   • After installation, close the terminal and open a new one to ensure that the changes to your PATH are applied.

8. Verify the Installation:

   • Open a new terminal window and type the following command to verify that Conda is installed correctly:

     conda --version
     

9. Update Conda (Optional):

   • It's a good practice to update Conda to the latest version after installation. Run the following command to update Conda:

     conda update conda
     

Installing Packages with Conda

1. Open the terminal and navigate to the directory where you want to run Epictope.

2. Create a new Conda environment for Epictope by running the following command:

conda create -n epictope

3. Activate the newly created environment by running:

conda activate epictope

4. Install the required dependencies by running the following commands:

conda install -c bioconda blast muscle
conda install -c salilab dssp
conda install -c conda-forge r-base r-stringi r-openssl r-remotes

Epictope R package

1. Starting R Inside the Conda Environment

   • Open the Terminal and activate your 'epictope' environment by typing the following command and pressing Enter:

     conda activate epictope

   • Your prompt should now show (epictope) at the beginning of the line, indicating you're inside the 'epictope' environment.

2. Installing the Epictope R Package

   • To install the Epictope R package using the "remotes" package, you can run R commands directly from the terminal using the R -e option.

   • Type the following commands into the terminal and press Enter:

     R -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes'); remotes::install_github('FriedbergLab/EpicTope')"

   • The R -e command allows you to execute R commands directly from the command line. The command above first checks if the "remotes" package is installed. If it's not, it will install it. Then it uses the "remotes" package to install the Epictope R package from GitHub.

   • Installation might take a few moments. If prompted to update any packages, type "Y" and press Enter to say "yes".

3. Verifying the Installation

   • Once the Epictope R package is installed, you should verify the installation by trying to load the package from the terminal.

   • Type the following command into the terminal and press Enter:

     R -e "library(epictope)"

   • If the command runs without displaying any error messages, that means the Epictope package was successfully installed and loaded.

Remember, you can deactivate your Conda environment when you're done by typing conda deactivate into the terminal and pressing Enter.

4. Downloading scripts

Now you are ready to execute the wget commands to download the Epictope workflow scripts. Copy each command one by one and paste it into terminal. Press Enter to run each command. The wget command is used to download files from the internet and save them to your current directory.

Download "single_score.R":

wget "https://raw.githubusercontent.com/FriedbergLab/EpicTope/main/scripts/single_score.R" 

Download "plot_scores.R":

wget "https://raw.githubusercontent.com/FriedbergLab/EpicTope/main/scripts/plot_scores.R" 

Download "install.R":

wget "https://raw.githubusercontent.com/FriedbergLab/EpicTope/main/scripts/install.R" 

Download "config_defaults.R":

wget "https://raw.githubusercontent.com/FriedbergLab/EpicTope/main/scripts/config_defaults.R" 

](https://github.com/FriedbergLab/Epictope?tab=readme-ov-file#methodology)