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Fixes and improvements to the installation instructions #447

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10101f7
Fix export $LD_LIBRARY_PATH in Installation.md
jkosinski May 19, 2024
1d89780
Fix <dest> that would not render in github markdown in Installation.md
jkosinski May 19, 2024
6deee72
just a clarification in Installation.md that was not clear to me
jkosinski May 19, 2024
c02a367
Add the actual OpenFold installation step in Installation.md
jkosinski May 19, 2024
9f2a2f8
Delete extra ` in Installation.md
jkosinski May 19, 2024
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14 changes: 8 additions & 6 deletions docs/source/Installation.md
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Expand Up @@ -19,16 +19,18 @@ At this time, only Linux systems are supported.
Mamba is recommended as the dependencies required by OpenFold are quite large and mamba can speed up the process.
- Activate the environment, e.g `conda activate openfold_env`
1. Run the setup script to configure kernels and folding resources.
> scripts/install_third_party_dependencies.sh`
> scripts/install_third_party_dependencies.sh
1. Prepend the conda environment to the `$LD_LIBRARY_PATH`., e.g.
`export $LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`. You may optionally set this as a conda environment variable according to the [conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to activate each time the environment is used.
1. Download parameters. We recommend using a destination as `openfold/resources` as our unittests will look for the weights there.
`export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`. You may optionally set this as a conda environment variable according to the [conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables) to activate each time the environment is used.
1. Download parameters. We recommend using a destination as `openfold/resources` as our unittests will look for the weights there. You can download all parameters to the same destination folder as the files will not overwrite each other.
- For AlphaFold2 weights, use
> ./scripts/download_alphafold_params.sh <dest>
> ./scripts/download_alphafold_params.sh &lt;dest&gt;
- For OpenFold weights, use :
> ./scripts/download_openfold_params.sh <dest>
> ./scripts/download_openfold_params.sh &lt;dest&gt;
- For OpenFold SoloSeq weights, use:
> ./scripts/download_openfold_soloseq_params.sh <dest>
> ./scripts/download_openfold_soloseq_params.sh &lt;dest&gt;
1. Install OpenFold:
> python setup.py install

### Checking your build with unit tests:

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