install_dependencies.py

import subprocess
import os

def install_packages(packages):
    for package in packages:
        try:
            # Construct the mamba install command
            command = ['mamba', 'install', '-y', package]
            print("Installing {}...".format(package))
            # Execute the command
            subprocess.check_call(command)
            print("{} installed successfully.".format(package))
        except subprocess.CalledProcessError as e:
            print("Failed to install {}: {}".format(package, e))

def merge_plantgeneclusterprots_fasta():
    input_dir = 'antismash/generic_modules/clusterblast'
    input_prefix = 'plantgeneclusterprots_part_'
    output_file = 'plantgeneclusterprots.fasta'

    if os.path.exists(os.path.join(input_dir, output_file)):
        print("plantgeneclusterprots.fasta already exists")
        return

    input_files = sorted(f for f in os.listdir(input_dir) if f.startswith(input_prefix))

    with open(os.path.join(input_dir, output_file), 'w') as outfile:
        for fname in input_files:
            file_path = os.path.join(input_dir, fname)
            with open(file_path) as infile:
                outfile.write(infile.read())

    print("merged plantgeneclusterprots.fasta")

    for fname in input_files:
        file_path = os.path.join(input_dir, fname)
        os.remove(file_path)

if __name__ == "__main__":
    merge_plantgeneclusterprots_fasta()

    # List of packages to be installed
    packages_to_install = [
        'glimmer',
        'glimmerhmm',
        'hmmer2',
        'hmmer=3.1b2',
        'fasttree=2.1.8',
        'diamond=0.8.9=boost1.60_1',
        'muscle=3.8.31',
        'prodigal',
        'blast=2.2.31',
        'cd-hit=4.6.6',
        'xz=5.2.2',
        'libxml2=2.9.3',
        "pplacer",
        'biopython == 1.76',
        'backports.lzma',
        "ncbi-datasets-cli",
        "unzip"
    ]

    # Install the packages
    install_packages(packages_to_install)

    command = ['pip', 'install', "-r", "requirements.txt"]
    print("pip installing requirements in requirements.txt...")
    subprocess.check_call(command)

    # have put graphlan in plantismash folder ahead in case of permission issue
    # command = ["git", "clone", "https://github.com/biobakery/graphlan.git"]
    # print("Cloning graphlan repository...")
    # subprocess.check_call(command)
    command = ["pip", "install", "graphlan/."]
    print("Installing graphlan...")
    subprocess.check_call(command)

    print("python2 run_antismash.py -h")
    subprocess.check_call(["python2", "run_antismash.py", "-h"])
    print("if any errors, please use conda list to check any missing dependencies and install those manually")
    # unable use nrpspks in specific_modules from antismash, but that is not for plantismash, so it was deleted
    print("!! genefinding module cannot work, so --genefinding none is default now!!")