Script to solve the package dependency issues for RoseTTAFold2NA.
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 Issues #104, #99, #94, #93, #37, #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
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 above create_env.sh script.
Also documented are the conda YAML (not tested) and conda table of packages.
Hope this is helpful!
Created a Databases file to download them in parallel, since some of them can be a slow download and take several days. The below command spawns 4 wget processes, and each process handles one file download, logging is quieted.
cat databases.txt | xargs -n 1 -P 4 wget -q