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motu-tool / mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling
GNU General Public License v3.0
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Possible to cache DB? #100

Closed wwood closed 1 year ago

wwood commented 1 year ago

Hi,

I'm attempting to benchmark some different profilers, and as part of this, I'm copying the database (and reads) to local disk, so that the processes are less IO-bound and so there is less noise in the benchmark from random happenings of others on the HPC.

Is there a way to specify where the DB mOTUs should use is? Also, I was too lazy to look at the code - where does downloadDB actually put the download, so I know what to copy? I'm using a conda install if that helps.

Thanks, ben

AlessioMilanese commented 1 year ago

Hi Ben,

Is there a way to specify where the DB mOTUs should use is?

You can use the -db command to specify the directory.

where does downloadDB actually put the download, so I know what to copy?

mOTUs is installed as a python package into one of the site-packages folders - The exact location depends on the exact pip command. The database is in the subfolder of the mOTUs package folder.

Here is the command to find the location of the site-packages

python -m site
wwood commented 1 year ago

Excellent, thanks.

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

From: Alessio Milanese @.> Sent: Tuesday, November 1, 2022 5:00:45 PM To: motu-tool/mOTUs @.> Cc: Ben J Woodcroft @.>; Author @.> Subject: Re: [motu-tool/mOTUs] Possible to cache DB? (Issue #100)

Hi Ben,

Is there a way to specify where the DB mOTUs should use is?

You can use the -db command to specify the directory.

where does downloadDB actually put the download, so I know what to copy?

mOTUs is installed as a python package into one of the site-packages folders - The exact location depends on the exact pip command. The database is in the subfolder of the mOTUs package folder.

Here is the command to find the location of the site-packages

python -m site

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