Installation
Miniconda
AutoEpiCollect is best run using Python 3.8.x. In order to have the required dependencies for AutoEpiCollect to run smoothly, we strongly recommend that you install Miniconda, the lighter version of Anaconda Python distribution. Miniconda is used to create multiple virtual Python environments, which are run on separate projects that require different dependencies. Following these steps will allow you to create a virtual environment with the exact dependencies needed. It is possible to run AutoEpiCollect by installing each dependency one by one, but we recommend following the steps outlined in this guide to set up AutoEpiCollect with minimal effort.
First, check if a version of Miniconda or Anaconda is installed in your system path and is compatible with AutoEpiCollect. If you are on macOS or Linux, open Terminal. If you are on Windows, open Anaconda Prompt, if installed (if not installed, this means you must download Miniconda). Run the following command::
conda search python
If a list of Python versions >=3.8.0 appear, you may skip the rest of the Miniconda installation and proceed to the next section.
Linux
To install Miniconda on Linux, run the following commands in Terminal::
cd ~
mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh
Windows
To install Miniconda on Windows, run the following commands in Command Prompt::
cd %HOMEPATH%
curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe
start /wait "" miniconda.exe /S
del miniconda.exe
macOS
To install Miniconda on macOS, run the following commands in Terminal::
cd ~
mkdir -p ~/miniconda3
curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -o ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh
Note: These commands install the latest Miniconda compatible with 64-bit Linux and Windows systems, as well as Apple Silicon M1/M2. If you have an older architecture or the commands above are not working properly, please go to the Miniconda installation website, download the Python 3.x installer compatible with your system, open the downloaded file, and follow the instructions to finish the Miniconda installation.
Java
Two of the tools required for AutoEpiCollect's population coverage analysis are PCOptim and PCOptim-CD. These programs, developed by Savsani and Kim et al., are coded in Java1,2. Please run the code below on your Terminal or Command Prompt to check if Java is already installed on your system::
java --version
If a Java version number 17 or greater appears, you can move on to the next section. Otherwise, please watch the videos linked below to install Java on your operating system. Make sure to set the Java home path in accordance with the videos.
Git
Git is a version control system that tracks changes in computer files, mainly source code. AutoEpiCollect is hosted on GitHub, a platform that stores Git repositories. Installing Git will allow you to easily download the most up-to-date files needed to successfully run AutoEpiCollect from Terminal or Command Prompt. First, check if you already have Git installed on your system by running the following command in your Terminal or Command Prompt::
git --version
If the Git version number appears, then you can move on to the AutoEpiCollect installation process. If not, then please navigate to the Git downloads website and follow the instructions to complete the installation process. During the installation process, select all the default or recommended settings.
Install AutoEpiCollect
Note: For Windows users. Anaconda Prompt is a shell program similar to Command Prompt that gives users access to command line input. Anaconda Prompt comes with the Miniconda installation and is necessary for running Git commands and creating your virtual environments. For the next steps of installing AutoEpiCollect and running the program, please use the Anaconda Prompt shell found by searching "miniconda3" in your start menu and clicking the Anaconda Prompt program.
To install AutoEpiCollect, you will need to copy all the necessary files from AutoEpiCollect's GitHub repository. Then, you must enter AutoEpiCollect's directory to access all the main files and programs. Enter the commands below in Terminal or Anaconda Prompt (on Windows) to gain access to AutoEpiCollect's directory::
First, navigate to your home directory.
Windows:
cd %HOMEPATH%
Mac and Linux:
cd ~
Next, download the AutoEpiCollect folder from the GitHub repository.
git clone https://github.com/mvsamudrala/AutoEpiCollect
cd AutoEpiCollect
As stated in the Miniconda section of the installation process, the use of a conda virtual environment to install all the packages needed for AutoEpiCollect to run smoothly is highly recommended. Located in the AutoEpiCollect directory is a .yml file that contains the necessary dependencies for creating a conda virtual environment compatible with AutoEpiCollect. Follow the commands below to create and activate this virtual environment on your machine::
conda env create -n aec_venv
conda activate aec_venv
Note: Creating the virtual environment might take some time depending on your machine. Please be prepared to wait up to 30 minutes after entering the first command for all the required dependencies to be installed.
If you wish to switch back to your default environment, run this command to deactivate the existing virtual environment::
conda deactivate
ChromeDriver
AutoEpiCollect uses in-silico tools to collect essential epitope data for ranking and filtration processes. Some of these in-silico tools are operated through webscraping functions encoded into AutoEpiCollect. The web scraping functionalities rely on ChromeDriver, a specialized program that enables automated web scraping specifically tailored for the Chrome browser. If not downloaded already, please download and use Chrome as the browser of choice for AutoEpiCollect. Next, follow the steps below to download the correct version of ChromeDriver for your machine.
- Update Chrome to its most current version by clicking the three dots in the upper right corner and checking to see if any update is available.
- Navigate to this website, https://chromedriver.chromium.org/downloads/version-selection, and click on the Chrome for Testing (CfT) availability dashboard. Here you will find the latest stable version of ChromeDriver.
- Click on the link for "Stable" and find the chromedriver binary matching the platform of your system. Refer to the table below to see which platform matches your machine's specifications.
| Specification | Platform |
|---|---|
| Macs with Apple Silicon | mac-arm64 |
| Macs with Intel Chips | mac-x64 |
| Windows 32-bit | win32 |
| Windows 64-bit | win64 |
| Linux 64-bit | linux64 |
- Copy and paste the link next to your chosen binary to download a zip file with the ChromeDriver program.
- Open the zip file and look into the folder to find the chromedriver executable file.
- This final step is crucial for AutoEpiCollect to use ChromeDriver. Move the chromedriver executable into the downloaded AutoEpiCollect folder.
Excel
AutoEpiCollect outputs its results in .xlsx spreadsheets that can be opened with Microsoft Excel. Please make sure you have Excel downloaded on your machine before running AutoEpiCollect so that you can view your final results.
You should now have all the dependencies needed to successfully run AutoEpiCollect. Please click the User Guide tab above to read the user guide and learn about all of AutoEpiCollect's functionalities.
References
- Savsani, K., Jabbour, G., & Dakshanamurthy, S. (2021). A New Epitope Selection Method: Application to Design a Multi-Valent Epitope Vaccine Targeting HRAS Oncogene in Squamous Cell Carcinoma. Vaccines, 10(1), 63. https://doi.org/10.3390/vaccines10010063
- Kim, M., Savsani, K., & Dakshanamurthy, S. (2023). A Peptide Vaccine Design Targeting KIT Mutations in Acute Myeloid Leukemia. Pharmaceuticals, 16(7), 932. https://doi.org/10.3390/ph16070932