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Building and using local databases #113

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rohitfarmer opened this issue Oct 8, 2022 · 2 comments
Open

Building and using local databases #113

rohitfarmer opened this issue Oct 8, 2022 · 2 comments

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@rohitfarmer
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rohitfarmer commented Oct 8, 2022 •
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Hi there; thank you, for this software. It's amazing. I can run it on the HPC; however, since I am working with a large number of sequences mmseq server is putting rate limits. I have started downloading the databases using:

wget https://raw.githubusercontent.com/sokrypton/ColabFold/main/setup_databases.sh
chmod +x setup_databases.sh
./setup_databases.sh database/

and wondering if there is a tutorial that I can follow on what to do once I have the databases to run everything locally.

Any suggestion would be helpful. Thanks!

PS: I am using version 1.3
@kfletcher88
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Did you find a solution? How about this section of the README?
https://github.com/sokrypton/ColabFold/blob/main/README.md#generating-msas-for-large-scale-structurecomplex-predictions

It looks like colabfold_search should produce the msa that can then be provided to colabfold_batch

@dbolser
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dbolser commented Feb 26, 2024

Check this and report back:
sokrypton/ColabFold#563

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@dbolser @kfletcher88 @rohitfarmer