Installation with singularity

[imu93]

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!

[mamunoz1]

Hi, I had the same problem (with the colabfold_1.5.5-cuda12.2.2.sif)

This works for me to resolve the problem. The CURL_CA_BUNDLE is located in /etc/ssl/certs/ca-certificates.crt instead of /etc/pki/tls/certs/ca-bundle.crt

I have the SIF file downloaded, and I'm working in a virtual environment, then I run: export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt

After that, the certificate was found with no problem, and it ran the download. I hope this helps.