Merge pull request PolusAI#258 from misterbrandonwalker/openfold

openfold

cwl_adapters/openfold.cwl

@@ -0,0 +1,140 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+
+class: CommandLineTool
+
+label: OpenFold Inference
+
+doc: |-
+  OpenFold Inference using a pre-trained model.
+
+baseCommand: ['python3', '/opt/openfold/run_pretrained_openfold.py']
+
+hints:
+  cwltool:CUDARequirement:
+    cudaVersionMin: "10.2"
+    cudaComputeCapability: "3.0"
+    cudaDeviceCountMin: 1
+    cudaDeviceCountMax: 1
+  DockerRequirement:
+    dockerPull: polusai/openfold-tool@sha256:84e1bb34f9d7ccfbd670e76d3f602334960f65ac091f96e9956ceeef985a9ffe
+    dockerOutputDirectory: /app
+
+requirements:
+  EnvVarRequirement:
+    envDef:
+      CONDA_PREFIX: /opt/conda/ 
+      # needed because https://github.com/aqlaboratory/openfold/blob/6f63267114435f94ac0604b6d89e82ef45d94484/scripts/utils.py#L9
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.input_fasta_dir)
+      - $(inputs.template_mmcif_dir)
+      - $(inputs.BASE_DATA_DIR)
+      - $(inputs.PARAMS_DIR)
+
+inputs:
+
+  PARAMS_DIR:
+    type: Directory
+    doc: "Directory containing OpenFold model parameter files."
+
+  BASE_DATA_DIR:
+    type: Directory
+    doc: "Directory containing OpenFold databases."
+
+  input_fasta_dir:
+    type: Directory
+    doc: "Directory containing OpenFold input fasta sequence."
+
+  template_mmcif_dir:
+    type: Directory
+    doc: "MMCIF files to use for template matching. This directory is required even if using template free inference."
+
+  input_fasta_dir_string:
+    type: string?
+    inputBinding:
+      position: 1
+    default: /app/fasta
+
+  template_mmcif_dir_string:
+    type: string?
+    inputBinding:
+      position: 2
+    default: /app/mmcif_files
+
+  output_dir:
+    type: string
+    inputBinding:
+      prefix: --output_dir
+    default: "/app"
+    doc: "Need to stage outputs in container in a specified directory"
+
+  openfold_checkpoint_path:
+    type: string?
+    inputBinding:
+      prefix: --openfold_checkpoint_path
+    default: /app/params/finetuning_ptm_1.pt
+    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"
+
+  config_preset:
+    type: string?
+    inputBinding:
+      prefix: --config_preset
+    default: "finetuning_ptm"
+    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."
+
+  uniref90_database_path:
+    type: string?
+    inputBinding:
+      prefix: --uniref90_database_path
+    default: /app/openfold_databases/uniref90/uniref90.fasta
+    doc: "For alignments to Uniref90 dataset."
+
+  mgnify_database_path:
+    type: string?
+    inputBinding:
+      prefix: --mgnify_database_path
+    default: /app/openfold_databases/mgnify/mgy_clusters_2022_05.fa
+    doc: "For alignments to  Mgnify, dataset."
+
+  pdb70_database_path:
+    type: string?
+    inputBinding:
+      prefix: --pdb70_database_path
+    default: /app/openfold_databases/pdb70/pdb70
+    doc: "For template matching to PDB70 database"
+
+  uniclust30_database_path:
+    type: string?
+    inputBinding:
+      prefix: --uniclust30_database_path
+    default: /app/openfold_databases/uniclust30/uniclust30_2018_08/uniclust30_2018_08
+    doc: "For template matching to Uniclust30 database"
+
+  bfd_database_path:
+    type: string?
+    inputBinding:
+      prefix: --bfd_database_path
+    default: /app/openfold_databases/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
+    doc: "For alignments to BFD dataset."
+
+  model_device:
+    type: string?
+    inputBinding:
+      prefix: --model_device
+    default: "cuda:0"
+
+outputs:
+  output_files:
+    type: File[]
+    outputBinding:
+      glob: "/app/predictions/*"
+
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- 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 .
+FROM nvidia/cuda:11.3.1-cudnn8-devel-ubuntu18.04
+
+RUN apt-key del 7fa2af80
+RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
+RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
+
+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
+RUN wget -P /tmp \
+    "https://github.com/conda-forge/miniforge/releases/download/23.3.1-1/Miniforge3-Linux-x86_64.sh" \
+    && bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda \
+    && rm /tmp/Miniforge3-Linux-x86_64.sh
+ENV PATH /opt/conda/bin:$PATH
+
+WORKDIR /opt/
+
+RUN git clone https://github.com/aqlaboratory/openfold.git
+
+WORKDIR /opt/openfold
+
+RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
+RUN export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}
+RUN wget -q -P /opt/openfold/openfold/resources \
+    https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
+RUN python3 setup.py install
+
+# by default openfold looks for parameters in the resources directory
+RUN mkdir resources
+
+RUN bash scripts/download_alphafold_params.sh resources

examples/openfold/openfold.wic

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