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Installation

To get started, set up a new python environment by following the installation instructions below.

We have tested gRNAde on Linux systems with Python 3.10.12 and CUDA 11.8/12.1 on NVIDIA A100 80GB GPUs and Intel XPUs, as well as on MacOS (CPU).

Clone repository and create new python environment

# Clone gRNAde repository
cd ~/  # or change this to your prefered download location
git clone https://github.com/chaitjo/geometric-rna-design.git
cd geometric-rna-design

# Create new environment and activate it
mamba create -n rna python=3.10
mamba activate rna
# (you can use conda/virtualenv instead of mamba)

Install packages and dependencies

# Install Pytorch (ensure appropriate CUDA version for your hardware)
pip install torch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 --index-url https://download.pytorch.org/whl/cu121

# Install Pytorch Geometric (ensure matching torch + CUDA version to PyTorch)
pip install torch-scatter -f https://data.pyg.org/whl/torch-2.1.0+cu121.html
pip install torch-sparse -f https://data.pyg.org/whl/torch-2.1.0+cu121.html
pip install torch-cluster -f https://data.pyg.org/whl/torch-2.1.0+cu121.html
pip install torch-geometric

# Install other python libraries
mamba install jupyterlab matplotlib seaborn pandas biopython biotite -c conda-forge
pip install wandb gdown pyyaml ipdb python-dotenv tqdm cpdb-protein torchmetrics einops ml_collections mdanalysis MDAnalysisTests draw_rna arnie

Download model checkpoints for gRNAde and RibonanzaNet

Model checkpoints are available on HuggingFace: https://huggingface.co/chaitjo/gRNAde

# Ensure you are in the base directory
cd ~/geometric-rna-design

# Install HuggingFace CLI (https://huggingface.co/docs/huggingface_hub/main/en/guides/cli)
curl -LsSf https://hf.co/cli/install.sh | bash
# alternate: pip install -U "huggingface_hub", or brew install huggingface-cli
hf auth login

# Download all checkpoints: gRNAde, RibonanzaNet, RibonanzaNet-SS, and RhoFold (unused)
hf download chaitjo/gRNAde --local-dir checkpoints/

The RhoFold checkpoint is optional, and not used by default.

Create an env file

Once your python environment is set up, create your .env file with the appropriate environment variables.

cd ~/geometric-rna-design/
touch .env

An example .env.example file is available (copy-paste contents into your .env file):

export PROJECT_PATH='/home/ckj24/geometric-rna-design/'
export DATA_PATH='/home/ckj24/geometric-rna-design/data/'
export WANDB_PROJECT='gRNAde'
export WANDB_ENTITY='chaitjo'
export WANDB_DIR='/home/ckj24/geometric-rna-design/'

Set up optional tools and dependencies

Extra tools and dependencies, used primarily for data preparation.

# (Optional) Install EternaFold for secondary structure prediction
cd ~/geometric-rna-design/tools/
git clone --depth=1 https://github.com/eternagame/EternaFold.git && cd EternaFold/src
make
# Notes: 
# - Multithreaded version of EternaFold did not install for me
# - To install on MacOS, start a shell in Rosetta using `arch -x86_64 zsh`

# (Optional) Install X3DNA for secondary structure determination
cd ~/geometric-rna-design/tools/
tar -xvzf x3dna-v2.4-linux-64bit.tar.gz
./x3dna-v2.4/bin/x3dna_setup
# Follow the instructions to test your installation

# (Optional) Install CD-HIT for sequence identity clustering
mamba install cd-hit -c bioconda

# (Optional) Install US-align/qTMclust for structural similarity clustering
cd ~/geometric-rna-design/tools/
git clone https://github.com/pylelab/USalign.git && cd USalign/ && git checkout 97325d3aad852f8a4407649f25e697bbaa17e186
g++ -static -O3 -ffast-math -lm -o USalign USalign.cpp
g++ -static -O3 -ffast-math -lm -o qTMclust qTMclust.cpp

# (Optional) Install ViennaRNA, mainly used for plotting in design notebook
cd ~/geometric-rna-design/tools/
tar -zxvf ViennaRNA-2.6.4.tar.gz
cd ViennaRNA-2.6.4
./configure  # ./configure --enable-macosx-installer
make
sudo make install