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uw-ipd / RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction
MIT License
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Irreproducible conda environment from yml file #81

Open pottsj21 opened 6 months ago

pottsj21 commented 6 months ago

As is, running the given yml file on conda 23.11.0 in my Linux system installed a cpu-only pytorch. Here's a fixed yml file that specifies a GPU-compatible Pytorch:

name: RF2NA
channels:
  - pytorch
  - nvidia
  - defaults
  - conda-forge
dependencies:
  - python=3.10
  - pip
  - pytorch::pytorch=2.0.1=py3.10_cuda11.7_cudnn8.5.0_0
  - requests
  - pytorch-cuda=11.7
  - dglteam/label/cu117::dgl
  - pyg::pyg
  - bioconda::mafft
  - bioconda::hhsuite
  - bioconda::blast
  - bioconda::hmmer>=3.3
  - bioconda::infernal
  - bioconda::cd-hit
  - bioconda::csblast
  - pip:
    - psutil
    - tqdm

and output from conda env export for a reproducible yml file is attached. Issue is similar to #36 , but here we want to run on GPU and not CPU. Additionally, you may want to add aria2 to the dependency list, as aria2c is recommended for downloading large dbs like bfd. env.txt