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uw-ipd / RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction
MIT License
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A SOLUTION for Package Dependency Issues 📦 #105

Open SuhasSrinivasan opened 2 months ago

SuhasSrinivasan commented 2 months ago

As of 2024-04-17, the main branch has many issues with unmet package dependencies, some examples below

NVTX functions not installed

Cannot load Graphbolt C++ library

Missing packages such as torchdata, pandas and pydantic

These issues have been documented at least in #104, #99, #36 and #33.

After quite a bit of trial and error, the following steps/script works for installing packages and is able to run through the example dataset.

Developed and tested on
OS: Ubuntu 22.04.4 LTS
Nvidia Driver: 550.54.15
CUDA: 12.4
conda: 24.3.0

This shell script takes care of dependencies in RF2na-linux.yml and SE3Transformer/requirements.txt i.e., a unified solution.

After cloning the RoseTTAFold2NA repository, place the below shell script in the RoseTTAFold2NA directory. Execute as $ source create_env.sh

All needed packages are installed, skip additional steps for SE3Transformer.

Download the script from this GitHub repo.

Hope this is helpful!

SuhasSrinivasan commented 2 months ago

Also documented are the conda YAML (not tested) and conda table of packages.

SuhasSrinivasan commented 2 months ago

📦 Submitted a Pull Request #110