INNER CODE UNIT · Python

check_install

BigDataBiology/SemiBin · SemiBin/main.py:639

def check_install(verbose, orf_finder=None, allow_missing_mmseqs2=False):
    '''Executes check_install subcommand, which checks for dependencies

    Parameters
    ----------
    verbose : boolean. If true, then prints out all the paths
    orf_finder : str, optional
    allow_missing_mmseqs2 : boolean, optional
        If true, then checks for mmseqs2
    '''
    import torch
    from shutil import which
    dependencies = [
                'bedtools',
                'hmmsearch',
                'FragGeneScan',
                'prodigal',  # prodigal needs to be checked after FragGeneScan
                'mmseqs',

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