iLund4u
Home page and documentation: https://art-egorov.github.io/ilund4u/
The Atkinson Lab 4U | AE
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    COMMAND-LINE PARAMETERS
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[POST-INSTALL STEPS]
--data
    Creates the 'ilund4u_data' folder in the current working directory.
    The folder contains adjustable configuration files used by iLund4u.
--linux
    Replaces the mmseqs path in the pre-made config file from the MacOS
    version [default] to the Linux version.
--mac
    Replaces the mmseqs path in the pre-made config file from the Linux
    version to the MacOS version.
--get-hmms
    Download HMMs (hmmscan format) of defence, anti-defence, virulence,
    and AMR proteins from our server [data-sharing.atkinson-lab.com]
--database <phages|plasmids>
    Download iLund4u database from our server [data-sharing.atkinson-lab.com].
    Available databases: "phages" and "plasmids" (see documentation for details)
[MISCELLANEOUS ARGUMENTS]
-h, --help
    Show this help message and exit.
-v, --version
    Show program version.
--debug
    Provide detailed stack trace for debugging purposes.
-q, --quiet
    Don't show progress messages.
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iLund4u can be used in three different modes:
1. ilund4u hotspots [parameters] - hotspot annotation.
2. ilund4u protein [parameters] - protein search versus iLund4u database.
3. ilund4u proteome [parameters] - proteome annotation and search versus
   iLund4u database.
To show mode-specific help messages use: ilund4u --help [mode]
(e.g. ilund4u --help hotspots)
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