setup.py

import subprocess

from setuptools import find_packages, setup


def install_blast():
    try:
        # Extract the downloaded archive
        subprocess.check_call(
            [
                "tar",
                "zxvf",
                "./resources/ncbi-blast-2.14.0+-x64-linux.tar.gz",
                "-C",
                "resources/",
            ]
        )

        # Add BLAST to the PATH
        blast_path = "resources/ncbi-blast-2.14.0+/bin"
        subprocess.check_call(
            ["echo", 'export PATH="$PATH:' + blast_path + '" >> ~/.bashrc']
        )

    except subprocess.CalledProcessError:
        print("Failed to install NCBI BLAST.")


def install_mafft():
    try:
        # Extract the downloaded archive
        subprocess.check_call(
            [
                "tar",
                "xvf",
                "./resources/mafft-7.505-with-extensions-src.tgz",
                "-C",
                "resources/",
            ]
        )

        mafft_core_dir = "./resources/mafft-7.505-with-extensions/core/"
        # Make MAFFT executable
        subprocess.check_call(["make", "clean"], cwd=mafft_core_dir)
        subprocess.check_call(["make"], cwd=mafft_core_dir)
        subprocess.check_call(["sudo", "make", "install"], cwd=mafft_core_dir)

    except subprocess.CalledProcessError:
        print("Failed to install MAFFT.")


# Call the BLAST installation function before installing your package
install_blast()

# Call the MAFFT installation function before installing your package
install_mafft()


setup(
    name="Alleleome",
    version="0.1.0",
    packages=find_packages(),
    install_requires=[
        "pandas == 2.0.0",
        "numpy==1.23.5",
        "biopython == 1.81",
    ],
    package_data={"Alleleome": ["sample_data/Oenococcus_oeni/*"]},
    entry_points={"console_scripts": ["Alleleome=Alleleome.cli:main"]},
)