- Moves python packages to conda installation

  instead of pip
- Adds helper line to automatically prepend conda library to
  $LD_LIBRARY_PATH

environment.yml

@@ -10,23 +10,25 @@ dependencies:
   - conda-forge::cudatoolkit==11.3.*
   - conda-forge::openmm=7.7.0
   - conda-forge::pdbfixer
+  - conda-forge::awscli
+  - conda-forge::biopython==1.79
+  - conda-forge::ninja
+  - conda-forge::numpy==1.21.2
+  - conda-forge::scipy==1.7.1
+  - conda-forge::pyyaml==5.4.1
+  - conda-forge::packaging
+  - conda-forge::tqdm==4.62.2
+  - conda-forge::typing-extensions==3.10.0.2
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
+  - bioconda::aria2
   - pytorch::pytorch=1.12.*
   - pip:
-      - packaging
-      - ninja==1.11.1
-      - biopython==1.79
       - deepspeed==0.5.10
       - dm-tree==0.1.6
       - ml-collections==0.1.0
-      - numpy==1.21.2
-      - PyYAML==5.4.1
       - requests==2.26.0
-      - scipy==1.7.1
-      - tqdm==4.62.2
-      - typing-extensions==3.10.0.2
       - pytorch_lightning==1.5.10
       - wandb==0.12.21
       - modelcif==0.7

scripts/install_third_party_dependencies.sh

@@ -8,16 +8,13 @@ wget -N --no-check-certificate -P openfold/resources \
 mkdir -p tests/test_data/alphafold/common
 ln -rs openfold/resources/stereo_chemical_props.txt tests/test_data/alphafold/common
 
-# echo "Downloading OpenFold parameters..."
-# bash scripts/download_openfold_params.sh openfold/resources
-# 
-# echo "Downloading AlphaFold parameters..."
-# bash scripts/download_alphafold_params.sh openfold/resources
-
 # Decompress test data
 gunzip -c tests/test_data/sample_feats.pickle.gz > tests/test_data/sample_feats.pickle
 
 python setup.py install
 
-# Setup LD_LIBRARY_PATH to include conda directory:
-export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`
+export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
+
+# The following will prepend conda library environment to $LD_LIBRARY_PATH
+# upon conda library activation 
+# conda env config vars set LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH