Removes conda installation from installation script.

environment.yml

@@ -7,14 +7,16 @@ dependencies:
   - conda-forge::python=3.9
   - conda-forge::setuptools=59.5.0
   - conda-forge::pip
+  - conda-forge::cudatoolkit==11.3.*
   - conda-forge::openmm=7.5.1
   - conda-forge::pdbfixer
-  - conda-forge::cudatoolkit==11.3.*
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
   - pytorch::pytorch=1.12.*
   - pip:
+      - packaging
+      - ninja==1.11.1
       - biopython==1.79
       - deepspeed==0.5.10
       - dm-tree==0.1.6
@@ -29,3 +31,4 @@ dependencies:
       - wandb==0.12.21
       - modelcif==0.7
       - git+https://github.com/NVIDIA/dllogger.git
+      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8bef

scripts/install_third_party_dependencies.sh

 #!/bin/bash
-CONDA_INSTALL_URL=${CONDA_INSTALL_URL:-"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"}
-
-source scripts/vars.sh
-
-# Install Miniconda locally
-rm -rf lib/conda
-rm -f /tmp/Miniconda3-latest-Linux-x86_64.sh
-wget -P /tmp \
-    "${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
-export PATH=lib/conda/bin:$PATH
-lib/conda/bin/python3 -m pip install nvidia-pyindex
-conda env create --name=${ENV_NAME} -f environment.yml
-source scripts/activate_conda_env.sh
-
-echo "Attempting to install FlashAttention"
-git clone https://github.com/HazyResearch/flash-attention
-CUR_DIR=$PWD
-cd flash-attention
-git checkout 5b838a8bef
-python3 setup.py install
-cd $CUR_DIR
 
 # Install DeepMind's OpenMM patch
 OPENFOLD_DIR=$PWD
-pushd lib/conda/envs/$ENV_NAME/lib/python3.9/site-packages/ \
+pushd $CONDA_DEFAULT_ENV/lib/python3.9/site-packages/ \
     && patch -p0 < $OPENFOLD_DIR/lib/openmm.patch \
     && popd
 
@@ -39,11 +14,13 @@ wget --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
+# 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