sokrypton / sokrypton/ColabFold
BioEmu Colab Notebook Dependency Installation Error + Workaround
Open
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
It seems that a change in Google Colab's environment affected the dependency installation in the BioEmu notebook.
In any case, I was able to run the model by replacing the code cell titled "Install dependencies" with the following:
import os
! pip install uv
! uv pip install bioemu[md]
os.system('wget https://mmseqs.com/foldseek/foldseek-linux-avx2.tar.gz; tar xvzf foldseek-linux-avx2.tar.gz')
I tested this with the T4 GPU using a short sequence and it seemed to work normally.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the BioEmu notebook and its cell titled "Install dependencies"; reproduce the dependency installation failure in Google Colab, then compare it with the reported workaround. Done means the notebook installs its dependencies and runs the model successfully on a short sequence with a T4 GPU.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics, tooling
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 45/100