Merge pull request #63 from schrodinger/conda-environment-yml

Install Script Installs All Dependencies at Once

environment.yml

+name: openfold_venv
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+dependencies:
+  - pip:
+      - biopython==1.79
+      - deepspeed==0.5.3
+      - 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==1.5.0
+      - nvidia-pyindex
+      - nvidia-dllogger
+  - pytorch::pytorch=1.10.*
+  - conda-forge::python=3.7
+  - conda-forge::setuptools=59.5.0
+  - conda-forge::pip
+  - conda-forge::openmm=7.5.1
+  - conda-forge::pdbfixer
+  - bioconda::aria2
+  - bioconda::hmmer==3.3.2
+  - bioconda::hhsuite==3.3.0
+  - bioconda::kalign2==2.04

requirements.txt

-biopython==1.79
-deepspeed==0.5.3
-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
-torch==1.10.0
-tqdm==4.62.2
-typing-extensions==3.10.0.2
-pytorch_lightning==1.5.0
-git+git://github.com/NVIDIA/dllogger.git

scripts/install_third_party_dependencies.sh

 #!/bin/bash
+CONDA_INSTALL_URL=${CONDA_INSTALL_URL:-"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"}
 
 source scripts/vars.sh
 
 # Install Miniconda locally
 rm -rf lib/conda
 rm -f /tmp/Miniconda3-latest-Linux-x86_64.sh
-wget -q -P /tmp \
-    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+wget -P /tmp \
+    "${CONDA_INSTALL_URL}" \
     && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p lib/conda \
     && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
 
 # Grab conda-only packages
-PATH=lib/conda/bin:$PATH
-conda update -qy conda \
-    && conda create --name $ENV_NAME -y python==3.7 \
-    && source lib/conda/etc/profile.d/conda.sh \
-    && conda activate $ENV_NAME \
-    && pip install -r requirements.txt \
-    && conda install -qy -c conda-forge \
-      openmm=7.5.1 \
-      pdbfixer
-
-# Comment out if you have these already installed on your system, for example in /usr/bin/
-conda install -c bioconda aria2
-conda install -y -c bioconda hmmer==3.3.2 hhsuite==3.3.0 kalign2==2.04
-
-pip install nvidia-pyindex
-pip install nvidia-dllogger
+export PATH=lib/conda/bin:$PATH
+conda env create --name=${ENV_NAME} -f environment.yml
+source activate ${ENV_NAME}
 
 # Install DeepMind's OpenMM patch
 OPENFOLD_DIR=$PWD