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rhysf / Synima

Synteny Imager
MIT License
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Specifying number of threads for BLAST+ to use #47

Open jamesdgalbraith opened 2 months ago

jamesdgalbraith commented 2 months ago

Hi, Thanks for the wonderful package, it's a lot easier to use than most of the synteny block detection and plotting pipelines. I'm curious if there's a built-in way to run the BLAST+ command with multiple threads. I've "forced" it by editing the blast command on line 58 of read_Blast.pm to also include -num_threads 32, but I'm not sure if this will break anything as I'm a Python and R user rather than a Perl user. Cheers, James.

rhysf commented 2 months ago

Dear @jamesdgalbraith ,

Thanks for your comment and glad to hear it has been useful.

I didn't have a built-in way to change threads, and i think the way you suggest sounds fine and shouldn't break anything. I have also gone ahead and added it as an optional parameter (-h) to the script Blast_grid_all_vs_all.pl, so you could also give that a try.

Best, Rhys