sokrypton / sokrypton/ColabFold
BioEmu run error
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- Dominant language
- Jupyter Notebook
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Description
Dear developers,
I wanted to try your recent notebook running bioemu, but I keep getting a bioemu installation related error, even though I separately do
!pip install bioemu
In this case, the running of the 3rd module gets stuck at:
Error: Command '['/root/.bioemu_colabfold/bin/python3', '-m', 'ensurepip', '--upgrade', '--default-pip']' returned non-zero exit status 1.
My guess is that calling bioemu from root somehow does not work.
It would be great if you have a look at this.
Thanks.
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 by reproducing the recent BioEmu notebook and its third module in the reported environment, including the separate pip install bioemu step. Investigate the ensurepip failure from /root/.bioemu_colabfold/bin/python3; done means the notebook's third module completes without the installation error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100