ovo.cli.init¶
Module Contents¶
Functions¶
Initialize the OVO home directory |
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Initialize nextflow, reference files and environment for the RFdiffusion preview workflow |
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Initialize nextflow, reference files and environment for the RFdiffusion end-to-end workflow |
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Initialize nextflow, reference files and environment for the ProteinQC workflow |
Data¶
API¶
- ovo.cli.init.app¶
‘Typer(…)’
- ovo.cli.init.RFDIFFUSION_MODEL_FILES¶
[(‘https://files.ipd.uw.edu/pub/RFdiffusion/6f5902ac237024bdd0c176cb93063dc4/Base_ckpt.pt’, ‘rfdiffu…
- ovo.cli.init.ALPHAFOLD_MODEL_FILES¶
[(‘https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar’, ‘alphafold_models’, ‘3…
- ovo.cli.init.ESM1V_MODEL_FILES¶
[(‘https://dl.fbaipublicfiles.com/fair-esm/models/esm1v_t33_650M_UR90S_1.pt’, ‘esm_models/esm1v_t33_…
- ovo.cli.init.ESM_IF_MODEL_FILES¶
[(‘https://dl.fbaipublicfiles.com/fair-esm/models/esm_if1_gvp4_t16_142M_UR50.pt’, ‘esm_models/esm_if…
- ovo.cli.init.BOLTZ_MODEL_FILES¶
None
- ovo.cli.init.home(home_dir: str | None = typer.Argument(None, help='OVO home directory'), yes: bool = typer.Option(False, '--yes', '-y', help='Confirm all without prompting'), no_env: bool = typer.Option(False, '--no-env', help='Do not set OVO_HOME in shell .bashrc/.zshrc file'), default_profile: str = typer.Option(None, '--profile', help='Default nextflow profile to use in default scheduler'))¶
Initialize the OVO home directory
- ovo.cli.init.preview()¶
Initialize nextflow, reference files and environment for the RFdiffusion preview workflow
- ovo.cli.init.rfdiffusion(scheduler: str = None)¶
Initialize nextflow, reference files and environment for the RFdiffusion end-to-end workflow
- ovo.cli.init.proteinqc(tool_keys: str = typer.Option('all', '--tools', help="Comma-separated list of ProteinQC tools to use, or 'all' to use all available tools (supported by the scheduler)"), scheduler: str = None)¶
Initialize nextflow, reference files and environment for the ProteinQC workflow