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sacdallago / bio_embeddings

Get protein embeddings from protein sequences
http://docs.bioembeddings.com
MIT License
460 stars 65 forks source link

I want to know the configuration of the people who run successfully #216

Open sudo349 opened 1 year ago

sudo349 commented 1 year ago

I always have strange mistakes

fedorn commented 1 year ago

It's working for me with the following conda's environment.yml:

name: bio-embeddings
channels:
  - conda-forge
dependencies:
  - python
  - pip
  - cudatoolkit=11.6
  - jax<0.2.0
  - jaxlib=0.1.55
  - pip:
    - jax-unirep==1.0.3
    - bio-embeddings[all]
    - kaleido
9las commented 1 year ago

I got the following error using the above config: Could not build wheels for jsonnet, which is required to install pyproject.toml-based projects But solved it by adding jsonnet to dependencies.

Also it seems like you do not need to specify the version of cudatoolkit. The latest version (11.8.0) seems to work fine:

name: bio-embeddings
channels:
  - conda-forge
dependencies:
  - python
  - pip
  - jsonnet
  - cudatoolkit
  - jax<0.2.0
  - jaxlib=0.1.55
  - pip:
    - jax-unirep==1.0.3
    - bio-embeddings[all]
    - kaleido