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AstrobioMike / GToTree

A user-friendly workflow for phylogenomics
GNU General Public License v3.0
204 stars 25 forks source link

Muscle Thread Usage #59

Closed raufs closed 2 years ago

raufs commented 2 years ago

Hi Mike,

Thanks for developing this awesome program!

For muscle align/super5 it seems the default is to use 20 threads when available, can you please have it's thread usage be controlled via the -n argument of GToTree.

It seems this can be done with the -threads argument:

https://drive5.com/muscle5/manual/cmd_super5.html

Kind regards, Rauf

AstrobioMike commented 2 years ago

Hey there, Rauf!

Thanks for the kind works and suggestion :)

I added a new flag for it (-M) just because i wanted to keep it separate from what is specifying for the HMM search (i know at least i would generally want this to be higher, while for the HMM searching, lower is fine). It is implemented as of version 1.6.35, which is already updated in conda 👍

Thanks again! -Mike

raufs commented 2 years ago

Wow that was fast! Thank you, that makes sense and sounds perfect!

Greatly appreciated! Rauf