Updates installation instructions in the README.
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README.md
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README.md
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@ -48,37 +48,17 @@ and one of {`jackhmmer`, [MMseqs2](https://github.com/soedinglab/mmseqs2) (night
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installed on on your system. You'll need `git-lfs` to download OpenFold parameters.
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installed on on your system. You'll need `git-lfs` to download OpenFold parameters.
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Finally, some download scripts require `aria2c` and `aws`.
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Finally, some download scripts require `aria2c` and `aws`.
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For convenience, we provide a script that installs Miniconda locally, creates a
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This package is currently supported for CUDA 11 and Pytorch 1.12
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`conda` virtual environment, installs all Python dependencies, and downloads
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useful resources, including both sets of model parameters. Run:
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```bash
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To install:
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scripts/install_third_party_dependencies.sh
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1. Clone the repository, e.g. `git clone https://github.com/aqlaboratory/openfold.git`
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```
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1. From the `openfold` repo:
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- Create an [Anaconda/Mamba](https://docs.anaconda.com/free/anaconda/install/index.html) environment, e.g. `conda env create -n openfold_env`
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- Activate the environment, e.g `conda activate openfold_env`
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1. Run `scripts/install_third_party_dependencies.sh` to configure kernels and folding resources.
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To activate the environment, run:
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For some systems, it may help to append the Conda environment library path to `$LD_LIBRARY_PATH`. The `install_third_party_dependencies.sh` script does this once, but you may need this for each bash instance.
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```bash
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source scripts/activate_conda_env.sh
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```
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To deactivate it, run:
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```bash
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source scripts/deactivate_conda_env.sh
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```
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With the environment active, compile OpenFold's CUDA kernels with
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```bash
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python3 setup.py install
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```
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To install the HH-suite to `/usr/bin`, run
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```bash
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# scripts/install_hh_suite.sh
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```
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## Usage
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## Usage
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