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Brandon Duane Walker
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openfold
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‎cwl_adapters/openfold.cwl‎

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.2
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class: CommandLineTool
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label: OpenFold Inference
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doc: |-
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OpenFold Inference using a pre-trained model.
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baseCommand: ['python3', '/opt/openfold/run_pretrained_openfold.py']
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hints:
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cwltool:CUDARequirement:
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cudaVersionMin: "10.2"
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cudaComputeCapability: "3.0"
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cudaDeviceCountMin: 1
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cudaDeviceCountMax: 1
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DockerRequirement:
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dockerPull: polusai/openfold-tool@sha256:84e1bb34f9d7ccfbd670e76d3f602334960f65ac091f96e9956ceeef985a9ffe
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dockerOutputDirectory: /app
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requirements:
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EnvVarRequirement:
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envDef:
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CONDA_PREFIX: /opt/conda/
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# needed because https://github.com/aqlaboratory/openfold/blob/6f63267114435f94ac0604b6d89e82ef45d94484/scripts/utils.py#L9
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InlineJavascriptRequirement: {}
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InitialWorkDirRequirement:
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listing:
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- $(inputs.input_fasta_dir)
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- $(inputs.template_mmcif_dir)
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- $(inputs.BASE_DATA_DIR)
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- $(inputs.PARAMS_DIR)
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inputs:
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PARAMS_DIR:
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type: Directory
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doc: "Directory containing OpenFold model parameter files."
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BASE_DATA_DIR:
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type: Directory
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doc: "Directory containing OpenFold databases."
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input_fasta_dir:
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type: Directory
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doc: "Directory containing OpenFold input fasta sequence."
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template_mmcif_dir:
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type: Directory
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doc: "MMCIF files to use for template matching. This directory is required even if using template free inference."
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input_fasta_dir_string:
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type: string?
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inputBinding:
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position: 1
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default: /app/fasta
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template_mmcif_dir_string:
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type: string?
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inputBinding:
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position: 2
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default: /app/mmcif_files
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output_dir:
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type: string
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inputBinding:
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prefix: --output_dir
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default: "/app"
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doc: "Need to stage outputs in container in a specified directory"
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openfold_checkpoint_path:
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type: string?
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inputBinding:
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prefix: --openfold_checkpoint_path
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default: /app/params/finetuning_ptm_1.pt
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doc: "Uses an checkpoint or parameter file. Expected types are Deepspeed checkpoint files or .pt files. Make sure your selected checkpoint file matches the configuration setting chosen in --config_preset"
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config_preset:
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type: string?
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inputBinding:
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prefix: --config_preset
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default: "finetuning_ptm"
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doc: "Specify a different model configuration. There are 5 available model preset settings, some of which support template modeling, others support template-free modeling. The default is model_1."
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uniref90_database_path:
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type: string?
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inputBinding:
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prefix: --uniref90_database_path
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default: /app/openfold_databases/uniref90/uniref90.fasta
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doc: "For alignments to Uniref90 dataset."
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mgnify_database_path:
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type: string?
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inputBinding:
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prefix: --mgnify_database_path
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default: /app/openfold_databases/mgnify/mgy_clusters_2022_05.fa
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doc: "For alignments to Mgnify, dataset."
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pdb70_database_path:
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type: string?
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inputBinding:
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prefix: --pdb70_database_path
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default: /app/openfold_databases/pdb70/pdb70
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doc: "For template matching to PDB70 database"
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uniclust30_database_path:
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type: string?
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inputBinding:
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prefix: --uniclust30_database_path
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default: /app/openfold_databases/uniclust30/uniclust30_2018_08/uniclust30_2018_08
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doc: "For template matching to Uniclust30 database"
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bfd_database_path:
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type: string?
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inputBinding:
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prefix: --bfd_database_path
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default: /app/openfold_databases/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
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doc: "For alignments to BFD dataset."
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model_device:
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type: string?
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inputBinding:
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prefix: --model_device
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default: "cuda:0"
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outputs:
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output_files:
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type: File[]
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outputBinding:
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glob: "/app/predictions/*"
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$namespaces:
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edam: https://edamontology.org/
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cwltool: http://commonwl.org/cwltool#
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$schemas:
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- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

‎examples/openfold/Dockerfile‎

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# docker build -f Dockerfile -t polusai/openfold-tool:0.1.0 .
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FROM nvidia/cuda:11.3.1-cudnn8-devel-ubuntu18.04
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RUN apt-key del 7fa2af80
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RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
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RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
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RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git
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RUN wget -P /tmp \
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"https://github.com/conda-forge/miniforge/releases/download/23.3.1-1/Miniforge3-Linux-x86_64.sh" \
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&& bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda \
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&& rm /tmp/Miniforge3-Linux-x86_64.sh
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ENV PATH /opt/conda/bin:$PATH
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WORKDIR /opt/
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RUN git clone https://github.com/aqlaboratory/openfold.git
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WORKDIR /opt/openfold
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RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
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RUN export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}
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RUN wget -q -P /opt/openfold/openfold/resources \
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https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
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RUN python3 setup.py install
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# by default openfold looks for parameters in the resources directory
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RUN mkdir resources
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RUN bash scripts/download_alphafold_params.sh resources

‎examples/openfold/openfold.wic‎

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steps:
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- id: openfold
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in:
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PARAMS_DIR: !ii '/polus2/OpenFold/openfold/openfold/resources/params'
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BASE_DATA_DIR: !ii '/polus2/OpenFold/openfold_databases'
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input_fasta_dir: !ii '/polus2/OpenFold/fasta'
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template_mmcif_dir: !ii '/polus2/OpenFold/mmcifs/pdb_mmcif/mmcif_files'
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out:
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- output_files: !& outputs

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