Fix environment.yml

Install prody with conda and not pip.

Author: jsilter

.gitignore

@@ -158,7 +158,7 @@ local_config.yml
 local_config_inference.yml
 local_config_filtering.yml
 temp1.py
-temp5.py
+temp2.py
 temp3.py
 temp4.py
 temp5.py

Dockerfile

@@ -1,7 +1,7 @@
 # Stage 1: Build Environment Setup
-FROM nvidia/cuda:11.7.1-devel-ubuntu22.04 as builder
+FROM nvidia/cuda:11.7.1-devel-ubuntu22.04 AS builder
 
-RUN apt-get update -y && apt-get install -y wget curl git tar bzip2 unzip && rm -rf /var/lib/apt/lists/*
+RUN apt-get update -y && apt-get install -y gcc wget curl git tar bzip2 unzip && rm -rf /var/lib/apt/lists/*
 
 # Create a user
 ENV APPUSER="appuser"
@@ -25,12 +25,6 @@ RUN ~/bin/micromamba env create --file $ENV_FILE_NAME && ~/bin/micromamba clean
 # Copy application code
 COPY --chown=$APPUSER:$APPUSER . $HOME/$DIR_NAME
 
-# Download models
-# These should download automatically on first inference
-# RUN curl -L -o diffdock_models_v1.1.zip "https://www.dropbox.com/scl/fi/drg90rst8uhd2633tyou0/diffdock_models.zip?rlkey=afzq4kuqor2jb8adah41ro2lz&dl=1" \
-#     && mkdir -p $HOME/$DIR_NAME/workdir \
-#     && unzip diffdock_models_v1.1.zip -d $HOME/$DIR_NAME/workdir
-
 
 # Stage 2: Runtime Environment
 FROM nvidia/cuda:11.7.1-runtime-ubuntu22.04

environment.yml

@@ -8,36 +8,35 @@ channels:
 dependencies:
   - python=3.9.18
   - pip
+  - python-devtools
   # Need older setuptools for openfold
   - setuptools=69.5.1
+  # ProDy needs to be installed with conda
+  - prody==2.2.0
+  - scipy==1.12.0
   # Need to install torch in order to build openfold, so install it first
   - pip:
     - --extra-index-url https://download.pytorch.org/whl/cu117
     - --find-links https://pytorch-geometric.com/whl/torch-1.13.1+cu117.html
     - torch==1.13.1+cu117
-  - pip:
-    - --extra-index-url https://download.pytorch.org/whl/cu117
-    - --find-links https://pytorch-geometric.com/whl/torch-1.13.1+cu117.html
     - dllogger @ git+https://github.com/NVIDIA/dllogger.git
     - e3nn==0.5.1
     - fair-esm[esmfold]==2.0.0
     - networkx==2.8.4
-    - openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307
     - pandas==1.5.1
-    - prody==2.2.0
-    - prody==2.2.0
     - pybind11==2.11.1
     - pytorch-lightning==1.9.5
     - rdkit==2022.03.3
     - scikit-learn==1.1.0
-    - scipy==1.12.0
     - torch==1.13.1+cu117
     - torch-cluster==1.6.0+pt113cu117
     - torch-geometric==2.2.0
     - torch-scatter==2.1.0+pt113cu117
     - torch-sparse==0.6.16+pt113cu117
     - torch-spline-conv==1.2.1+pt113cu117
     - torchmetrics==0.11.0
+  - pip:
+    - openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307
   - pip:
     - gradio==3.50.*
     - requests