fix issues with building Docker images (PolusAI#261)

Author: ndonyapour

cwl_adapters/autodock_vina_batch.cwl

@@ -52,7 +52,7 @@ arguments:
 
 hints:
   DockerRequirement:
-    dockerPull: jakefennick/autodock_vina
+    dockerPull: ndonyapour/autodock_vina
 
 requirements:
   InlineJavascriptRequirement: {}

cwl_adapters/autodock_vina_rescore.cwl

@@ -22,7 +22,7 @@ arguments:
 
 hints:
   DockerRequirement:
-    dockerPull: jakefennick/autodock_vina
+    dockerPull: ndonyapour/autodock_vina
 
 requirements:
   InlineJavascriptRequirement: {}

docker/dockerBuild.sh

@@ -19,7 +19,7 @@ cd examples/scripts/
 sudo docker build --no-cache --pull -f Dockerfile_align_protein_ca_mda -t jakefennick/align_protein_ca_mda .
 sudo docker build --no-cache --pull -f Dockerfile_align_protein_ca_pymol -t jakefennick/align_protein_ca_pymol .
 sudo docker build --no-cache --pull -f Dockerfile_atomselect -t jakefennick/atomselect .
-sudo docker build --no-cache --pull -f Dockerfile_autodock_vina -t jakefennick/autodock_vina .
+sudo docker build --no-cache --pull -f Dockerfile_autodock_vina -t ndonyapour/autodock_vina .
 sudo docker build --no-cache --pull -f Dockerfile_autodock_vina_filter -t ndonyapour/autodock_vina_filter .
 sudo docker build --no-cache --pull -f Dockerfile_bash_scripts -t jakefennick/bash_scripts .
 sudo docker build --no-cache --pull -f Dockerfile_calculate_net_charge -t jakefennick/calculate_net_charge .

dockerPull.sh

@@ -10,7 +10,7 @@ docker pull jakefennick/biosimspace
 docker pull jakefennick/align_protein_ca_mda
 docker pull jakefennick/align_protein_ca_pymol
 docker pull jakefennick/atomselect
-docker pull jakefennick/autodock_vina
+docker pull ndonyapour/autodock_vina
 docker pull ndonyapour/autodock_vina_filter
 docker pull jakefennick/bash_scripts
 docker pull jakefennick/calculate_net_charge

examples/scripts/Dockerfile_autodock_vina

@@ -1,8 +1,6 @@
-FROM condaforge/miniforge-pypy3
+FROM condaforge/miniforge3
+# NOT miniforge-pypy3 (The build process is incompatible with pypy)
 
-# The latest release version 1.2.3 has several known bugs.
-# See https://github.com/ccsb-scripps/AutoDock-Vina/pull/81
-# and https://github.com/ccsb-scripps/AutoDock-Vina/pull/138
 # RUN conda install -c conda-forge vina
 
 RUN apt-get update && apt-get install -y git

examples/scripts/Dockerfile_molgan

@@ -7,6 +7,9 @@ ENV RDKIT_ERROR_LOGGING="OFF"
 
 RUN apt-get update && apt-get install -y wget git
 
+# Install Python 3.10 using Mamba
+RUN mamba install -y python=3.10
+
 # Clone MolGAN
 RUN git clone https://github.com/ndonyapour/MolGAN.git
 
@@ -32,4 +35,4 @@ RUN bash data/download_dataset.sh data/gdb9.sdf data/NP_score.pkl.gz data/SA_sco
 RUN python utils/sparse_molecular_dataset.py --input_sdf_path data/gdb9.sdf --output_data_path data/data.pkl
 
 # Training step
-RUN python example.py --input_data_path data/data.pkl --num_epochs 10 --output_log_path log --input_NP_Score_path data/NP_score.pkl.gz  --input_SA_Score_path data/SA_score.pkl.gz --output_model_dir ./trained_models
+RUN python example.py --input_data_path data/data.pkl --num_epochs 2 --output_log_path log --input_NP_Score_path data/NP_score.pkl.gz  --input_SA_Score_path data/SA_score.pkl.gz --output_model_dir ./trained_models

examples/scripts/Dockerfile_onionnet-sfct

@@ -1,6 +1,8 @@
 FROM condaforge/miniforge3
 # NOT mambaforge-pypy3 (pandas & rdkit & mdtraj are incompatible with pypy)
 
+# Scikit-learn 1.0.2 is only compatible with 3.6 < python < 3.11
+RUN mamba install -y python=3.10
 # Install requirements
 RUN apt-get update && apt-get install -y wget git
 RUN mamba install -c conda-forge openbabel numpy pandas mdtraj biopandas -y