Installation Guide

Table of Contents

• C++ Executable File
• Python Library
  • Installation from Source
  • Installation from PyPI
  • Installation from BioConda

C++ Executable File

To install the executable version of NEFFy:

1. Clone the repository:

   git clone https://github.com/Maryam-Haghani/Neffy.git

2. Navigate to the project directory:

   cd Neffy

3. Compile the code using a C++ compiler that supports C++17 or a newer version, through the provided Makefile in the repository.

   make

   • If the make command is not available on your operating system, refer to the Help page.

Once the compilation is complete, you can run the program via the command line.
This package is cross-platform and works on Linux, Windows, and macOS without requiring additional compilation.

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Python Library

Installation from Source

To install the library from the source:

1. Clone the repository:

   git clone https://github.com/Maryam-Haghani/Neffy.git

2. Navigate to the project directory:

   cd Neffy

3. Ensure you have setuptools and wheel installed:

   pip install setuptools wheel

4. Build the source distribution and wheel:

   python setup.py sdist bdist_wheel

5. Install the package from the root directory of the project:

   pip install .

• Alternatively, you can install the package directly from the built wheel file (in the dist directory):

  pip install dist/neffy-0.1-py3-none-any.whl

Installation from PyPI

Our Python library is available on PyPI. This release provides pre-built, platform-specific wheels for Windows, Linux, and macOS, as well as a source distribution for building on other operating systems. This streamlines the installation and management process using pip.

• To install the package from PyPI, run:

  pip install neffy

Installation from BioConda:

You can also install neffy through BioConda by running the following commands:

conda config --add channels conda-forge
conda install -c bioconda neffy

The first command adds the conda-forge channel to your Conda configuration, which is necessary to access a broader range of packages and dependencies that might not be available on the default channels.

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For further assistance or inquiries, please contact the developer or create an issue in the GitHub repository.