Installation

HiTIPS has been installed and tested on Linux (Ubuntu), Windows (10 and above), and Mac using Intel processors. However, HiTIPS is currently not operational on Macs with Apple Chips (M1, M2, M3) even when using Rosetta.

If you are using Windows, make sure to install `Visual Studio <https://visualstudio.microsoft.com/>`_ and `Microsoft C++ Build Tools <https://visualstudio.microsoft.com/visual-cpp-build-tools/>`_ before installing HiTIPS.

If you are using Mac OS (Only Intel chip works for now), make sure to install `Xcode <https://developer.apple.com/xcode/>`_ before installing HiTIPS.

Hardware and Software Requirements

Hardware Requirements

  • CPU: Multi-core processor (e.g., Intel i7 or AMD Ryzen 7).

  • RAM: Minimum 16GB (32GB recommended for large datasets).

  • Storage: SSD with 500GB or more of available space.

  • GPU: Optional but recommended, especially if using CUDA-enhanced functionalities.

Software Requirements

  • Operating System: 64-bit Linux distribution (e.g., Ubuntu, CentOS, Fedora), Windows (10 and after)

  • Python: Version 3.9 or newer.

  • Package Manager: Latest version of Miniconda or Anaconda.

Installation

To install HiTIPS, we highly recommend using conda. To install conda, you must first pick the right installer for you. The following are the most popular installers currently available:

Miniconda

Miniconda is a minimal installer for Anaconda. Use this installer if you want to manage most packages yourself.

Anaconda Distribution

Anaconda Distribution is a full-featured installer that includes a suite of packages for data science, plus Anaconda Navigator, a GUI for managing conda environments.

Miniforge

Miniforge is maintained by the conda-forge community, preconfigured for the conda-forge channel. Learn more about conda-forge at their website.

Tip

If you are just starting out, we recommend installing conda via the Miniconda installer.

Installing HiTIPS Using Conda and Pip

This method has been tested on Linux (Ubuntu), Windows (10 and above), and Mac using Intel processors. However, this method is currently not working on Macs with Apple Chips (M1, M2, M3) even when using Rosetta.

  1. Create a Conda Environment:

    conda create --name hitips_env python=3.9
conda activate hitips_env

  2. Install HiTIPS using Pip:

    pip install hitips

  3. Launch HiTIPS:

    hitips

Installing HiTIPS Using Requirements File

This method has been tested on Linux (Ubuntu), Windows (10 and above), and Mac using Intel processors. However, this method is currently not working on Macs with Apple Chips (M1, M2, M3) even when using Rosetta.

  1. Clone the HiTIPS Repository:

    git clone https://github.com/CBIIT/HiTIPS.git

Navigate to the cloned HiTIPS directory before proceeding with the next steps.

  2. Create and Activate a Conda Environment:

    conda create --name hitips_env python=3.9
conda activate hitips_env

  3. Install HiTIPS using Pip from the Requirements File:

    pip install -r requirements.txt

The `requirements.txt` file can be accessed `here <https://github.com/CBIIT/HiTIPS/blob/main/requirements.txt>`__.

  4. Launch HiTIPS:

    python -m hitips.HiTIPS

Installing HiTIPS Using Docker

This method has been tested on Linux (Ubuntu), Windows (10 and above), and Mac using Intel processors. However, this method is currently not working on Macs with Apple Chips (M1, M2, M3) even when using Rosetta.

  1. Install Docker:

    Follow the official Docker installation instructions for your platform: https://docs.docker.com/get-docker/

  2. Install an X11 Server

  3. Configure the X11 Server

    • macOS (XQuartz): - After installing XQuartz, start it. - Go to XQuartz Preferences > Security and check “Allow connections from network clients”. - Restart XQuartz. - Open a terminal and run the following command to allow Docker to connect to XQuartz:

      xhost + 127.0.0.1

    • Windows (VcXsrv): - After installing VcXsrv, start it with the following options: - Multiple windows - Start no client - Extra settings: check “Disable access control” - Open a command prompt and run:

      set DISPLAY=host.docker.internal:0.0

    • Linux: - Ensure you have an X11 server installed and running. Most Linux distributions come with an X11 server pre-installed. - Open a terminal and run the following command to allow Docker to connect to your X server:

      xhost +local:docker

  4. Pull the HiTIPS Docker Image:

    docker pull adibkeikhosravi991/hitips:latest

  5. Run the Docker Container

    Now, you can run your Docker container with the correct display settings:

    • macOS:

      docker run -it --rm -e DISPLAY=host.docker.internal:0 -v /tmp/.X11-unix:/tmp/.X11-unix adibkeikhosravi991/hitips:latest

    • Windows:

      docker run -it --rm -e DISPLAY=host.docker.internal:0.0 -v /tmp/.X11-unix:/tmp/.X11-unix adibkeikhosravi991/hitips:latest

      Note: Ensure that host.docker.internal is resolvable within the Docker container. If it is not, you might need to use the IP address directly.

    • Linux:

      docker run -it --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix adibkeikhosravi991/hitips:latest