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UCLOrengoGroup / domain-annotation-pipeline

Data pipeline to provide consensus domain annotations for protein structures
GNU General Public License v3.0
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Issue encountered during installing UniDoc #2

Open housemiao opened 5 months ago

housemiao commented 5 months ago

Hi,

I came from the CATH-alphaflow google colab and was trying run the whole workflow. I have a problem that when I try to wget the UniDoc url in my terminal, it says that the issued certificate was expired for the url and therefore visit was forbidden (403). Is there anyway that I can sidestep this? Thanks in advance.

Best, House

bordin89 commented 5 months ago

Hi House,

The issue seems to be that the certificate on the UniDoc website has expired or that their website is down. I have the same issue as you, with the main website as well. Until they fix it on their end, unfortunately the're not much we can do. I'm attaching a copy of UniDoc so you can keep working on this.

Best Nicola UniDoc.tar.gz

bordin89 commented 5 months ago

The issue with this is that the code is written for a Jupyter notebook, so it seems that you’re not removing the ‘/’ that wraps the commands.

[A screenshot of a computer screen Description automatically generated]

I tried re-running the Colab notebook and everything works fine.

[A screen shot of a computer Description automatically generated]

Best, Nicola

-- Nicola Bordin, PhD Structural and Molecular Biology Darwin Building University College London Gower Street WC1E 6BT London UK orcid.org/0000-0002-6568-9035http://orcid.org/0000-0002-6568-9035

From: housemiao @.> Date: Tuesday, 9 April 2024 at 23:10 To: UCLOrengoGroup/domain-annotation-pipeline @.> Cc: Nicola Bordin @.>, Comment @.> Subject: Re: [UCLOrengoGroup/domain-annotation-pipeline] Issue encountered during installing UniDoc (Issue #2)

Got it! Thank you so much for the file. I have another error that when I nextflow run the annotation-pipeline.nf file, says "sed: 1: "chainsaw_results.csv": command c expects \ followed by text". I tried to find this line in the get_prediction.py file in chainsaw but failed and my chainsaw is able to run by itself. Do you have any clue what is the problem? Nextflow file?

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