sokrypton / sokrypton/ColabFold

Installation with singularity

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Description

Dear developers, I'm trying to run the colabfold container as specified here: https://github.com/sokrypton/ColabFold/wiki/Running-ColabFold-in-Docker

However, I'm having issues setting my cache directory:
singularity run -B /home/isaac12/scratch/colabfold_cache:/cache colabfold_1.5.3-cuda11.8.0.sif python -m colabfold.download

Traceback (most recent call last):
File "/usr/local/envs/colabfold/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/local/envs/colabfold/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/colabfold/download.py", line 58, in
download_alphafold_params("alphafold2_multimer_v3")
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/colabfold/download.py", line 42, in download_alphafold_params
response = requests.get(url, stream=True)
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/requests/adapters.py", line 458, in send
self.cert_verify(conn, request.url, verify, cert)
File "/usr/local/envs/colabfold/lib/python3.9/site-packages/requests/adapters.py", line 261, in cert_verify
raise OSError(
OSError: Could not find a suitable TLS CA certificate bundle, invalid path: /etc/pki/tls/certs/ca-bundle.crt

I wonder if you have any suggestions in this regard.
Thanks for your support!

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the linked Running ColabFold in Docker wiki page and the shown Singularity command, then inspect the traceback through colabfold/download.py and its requests call. Reproduce the missing CA bundle error in the container and determine the installation guidance or configuration change needed for the cache download to complete.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
devops, infrastructure
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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