Merge pull request #232 from misterbrandonwalker/patch_onion_build

patch onionnet build error

Author: Nicholas-Schaub

cwl_adapters/onionnet-sfct.cwl

@@ -9,7 +9,7 @@ baseCommand: ["python", "/OnionNet-SFCT/scorer.py"]
 
 hints:
   DockerRequirement:
-    dockerPull: cyangnyu/onionnet-sfct
+    dockerPull: polusai/onionnet-sfct-tool:1.0.0
 
 requirements:
   InlineJavascriptRequirement: {}
@@ -60,12 +60,12 @@ inputs:
 
   output_docking_score:
     type: string?
-  
+
   output_poses_rescore:
     type: string?
-    
+
 outputs:
-  
+
   output_score_path:
     type: File
     outputBinding:

docker/dockerBuild.sh

@@ -30,7 +30,7 @@ sudo docker build --no-cache --pull -f Dockerfile_remove_terminal_residue_name_p
 sudo docker build --no-cache --pull -f Dockerfile_rename_residues_mol -t jakefennick/rename_residues_mol .
 sudo docker build --no-cache --pull -f Dockerfile_combine_structure -t ndonyapour/combine_structure .
 sudo docker build --no-cache --pull -f Dockerfile_molgan -t ndonyapour/molgan .
-sudo docker build --no-cache --pull -f Dockerfile_onionnet-sfct -t cyangnyu/onionnet-sfct .
+sudo docker build --no-cache --pull -f Dockerfile_onionnet-sfct -t polusai/onionnet-sfct-tool:1.0.0 .
 sudo docker build --no-cache --pull -f Dockerfile_smina -t cyangnyu/smina .
 sudo docker build --no-cache --pull -f Dockerfile_pdbfixer -t ndonyapour/pdbfixer .
 sudo docker build --no-cache --pull -f Dockerfile_extract_protein -t ndonyapour/extract_protein .

examples/scripts/Dockerfile_onionnet-sfct

@@ -3,34 +3,20 @@ FROM condaforge/mambaforge
 
 # Install requirements
 RUN apt-get update && apt-get install -y wget git
-
-# Create environment
-# Since python 3.10 is already installed in the base image condaforge/mambaforge, 
-# if not specify the python version requirement, python version will has conflict with the openbabel <3.0.
-#0 23.40 Pinned packages:
-#0 23.40   - python 3.10.*
-#0 23.40 The following packages are incompatible
-#0 23.40 └─ openbabel <3.0  is installable with the potential options
-#0 23.40    ├─ openbabel 2.4.1 would require
-#0 23.40    │  └─ python >=2.7,<2.8.0a0 , which can be installed;
-#0 23.40    ├─ openbabel 2.4.1 would require
-#0 23.40    │  └─ python >=3.6,<3.7.0a0 , which can be installed;
-#0 23.40    └─ openbabel 2.4.1 would require
-#0 23.40       └─ python >=3.7,<3.8.0a0 , which can be installed.
-# So, explicitly downgrade to python=3.7.*
-RUN mamba install -c conda-forge "python=3.7.*" "openbabel<3.0" numpy pandas mdtraj biopandas -y
-RUN pip install -U scikit-learn rdkit-pypi
+RUN mamba install -c conda-forge openbabel numpy pandas mdtraj biopandas -y
+# model saved required scikit-learn==1.0.2
+RUN pip install -U scikit-learn==1.0.2 rdkit-pypi
 
 # cleanup
 RUN apt-get clean
 RUN mamba clean --all --yes
 RUN pip cache purge
 
 # Install OnionNet-SFCT
-RUN git clone https://github.com/cyangNYU/OnionNet-SFCT.git
+RUN git clone https://github.com/misterbrandonwalker/OnionNet-SFCT.git
 WORKDIR /OnionNet-SFCT
 
 # Download models
-RUN mkdir -p data && cd data && wget https://huggingface.co/cyangNYU/OnionNet-SFCT-final-model/resolve/main/sfct_std_final.model
+RUN mkdir -p data && cd data && wget -nv --no-clobber https://huggingface.co/cyangNYU/OnionNet-SFCT-final-model/resolve/main/sfct_std_final.model
 
 ADD Dockerfile_onionnet-sfct .