From a96a282e16e98e7ea58d00631b8adc80dec9db5b Mon Sep 17 00:00:00 2001
From: Brandon Duane Walker <walkerbd@UPDATEME.HOSTNAME.COM>
Date: Wed, 22 May 2024 16:40:32 -0400
Subject: [PATCH] openfold

---
 cwl_adapters/openfold.cwl      | 89 ++++++++++++++++++++++++++++++++++
 examples/generation/Dockerfile | 30 ++++++++++++
 2 files changed, 119 insertions(+)
 create mode 100644 cwl_adapters/openfold.cwl
 create mode 100644 examples/generation/Dockerfile

diff --git a/cwl_adapters/openfold.cwl b/cwl_adapters/openfold.cwl
new file mode 100644
index 0000000..d87e58f
--- /dev/null
+++ b/cwl_adapters/openfold.cwl
@@ -0,0 +1,89 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: OpenFold Inference
+
+baseCommand: ["python3", "run_pretrained_openfold.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: mrbrandonwalker/openfold-tool:0.1.0
+
+inputs:
+
+  input_fasta_dir:
+    type: Directory
+    inputBinding:
+      position: 1
+
+  mmcif_dir:
+    type: Directory
+    inputBinding:
+      position: 2
+
+  output_dir:
+    type: Directory
+    inputBinding:
+      prefix: --output_dir
+      position: 3
+
+  config_preset:
+    type: string?
+    default: model_1_ptm
+    inputBinding:
+      prefix: --config_preset
+
+  uniref90_database_path:
+    type: Directory
+    inputBinding:
+      prefix: --uniref90_database_path
+      position: 4
+
+  mgnify_database_path:
+    type: File
+    inputBinding:
+      prefix: --mgnify_database_path
+      position: 5
+
+  pdb70_database_path:
+    type: Directory
+    inputBinding:
+      prefix: --pdb70_database_path
+      position: 6
+
+  uniclust30_database_path:
+    type: Directory
+    inputBinding:
+      prefix: --uniclust30_database_path
+      position: 7
+
+  bfd_database_path:
+    type: File
+    inputBinding:
+      prefix: --bfd_database_path
+      position: 8
+
+  model_device:
+    type: string?
+    default: "cuda:0"
+    inputBinding:
+      prefix: --model_device
+
+outputs:
+
+  stdout:
+    type: File
+    outputBinding:
+      glob: stdout
+
+stdout: stdout
+
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
+
diff --git a/examples/generation/Dockerfile b/examples/generation/Dockerfile
new file mode 100644
index 0000000..9968cf4
--- /dev/null
+++ b/examples/generation/Dockerfile
@@ -0,0 +1,30 @@
+# docker build -f Dockerfile -t mrbrandonwalker/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
\ No newline at end of file