Installation Guide

Follow these steps to install SchemaRefinery. There are three methods to install SchemaRefinery: Bioconda, PyPI or using Git. Choose the one that is most convenient based on your system and preferences. Schema Refinery requires Python 3.9 or higher, BLAST+ and NCBI datasets to be installed.

Important

For a better organization of the packages and dependencies, it is advised to create a new conda environment to install Schema Refinery into.

Installation through Bioconda

  1. Install Conda: Ensure that Conda is installed on your system. You can install Miniconda (a minimal Conda installer) using the following commands:

    # For macOS and Linux
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

  2. Add Bioconda and conda-forge channels: Ensure that conda can search and install packages from the Bioconda and conda-forge channels.

    conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

  3. Create a Conda Environment: It is recommended to create a conda environment to manage dependencies:

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

  4. Install Schema Refinery:

    conda install bioconda::schemarefinery

Installation through PyPI

  1. Install pip: For Python 3.4 and higher installed using Windows or macOS pip is installed as default. For Linux environments run:

    #For Ubuntu and python3
sudo apt-get install python3 - pip

#For CentOS and python3
sudo yum install python3 - pip

  2. Install Conda: Ensure that Conda is installed on your system. You can install Miniconda (a minimal Conda installer) using the following commands:

    # For macOS and Linux
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

  3. Create a Conda Environment: It is recommended to create a conda environment to install Schema Refinery and manage dependencies.

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

  4. Install SchemaRefinery using pip:

    pip install SchemaRefinery

Installation through GitHub

  1. Install Git: Ensure that Git is installed on your system. You can install Git using the following command:

    # For macOS
brew install git

# For Ubuntu/Debian
sudo apt-get install git

# For Fedora
sudo dnf install git

  2. Install Conda: Ensure that Conda is installed on your system. You can install Miniconda (a minimal Conda installer) using the following commands:

    # For macOS and Linux
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

  3. Clone the Repository: Clone the SchemaRefinery repository from GitHub:

    git clone https://github.com/MForofontov/Schema_Refinery.git

  4. Change Directory: Navigate to the cloned repository:

    cd Schema_Refinery

  5. Create a Conda Environment: It is recommended to create a conda environment to manage dependencies:

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

  6. Install Dependencies: Install BLAST and the required Python packages:

    conda install blast
pip install -r requirements.txt

  7. Install Schema Refinery:

    python setup.py install

  8. Verify Installation: Verify the installation by running the following command:

    SR --help

Additional Information

  • Updating the Package: To update SchemaRefinery, navigate to the repository directory and pull the latest changes:

    cd Schema_Refinery
git pull
python setup.py install

  • Uninstalling the Package: To uninstall SchemaRefinery, use the following command:

    pip uninstall SchemaRefinery

Important

If you encounter any issues during installation, ensure that all dependencies are installed and that you are using a compatible version of Python. You can also refer to the GitHub repository for more information and support.