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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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Option to increase cd-hit-est memory limit #82

Closed ssnn-airr closed 2 years ago

ssnn-airr commented 3 years ago

Original report by Julian Zhou (Bitbucket: [Julian Zhou](https://bitbucket.org/Julian Zhou), ).

Currently, limit is hard-coded by default_max_memory = 3000 in presto/Applications.py to be 3000. It would be very helpful to provide an argument via ClusterSets to increase that limit. Thank you!

ssnn-airr commented 3 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Huh. That’s weird. I don’t recall why we did that. I’ll take a look at this soon - maybe this weekend?

ssnn-airr commented 3 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

I added the --mem argument to ClusterSets in e8a567e. I took the lazy route and just had it do nothing for usearch/vsearch, rather than figure out if there’s a way to calculate it. I tested that it ran, but didn’t test that it did anything useful…

ssnn-airr commented 2 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Assuming this is resolved by e8a567e.