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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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Sharing databases on a cluster and .dmanifest problem... #317

Closed geboro closed 2 years ago

geboro commented 2 years ago

Hello!

I'm teaching on a cluster and I'm trying to get other users to install checkM (which works I think), but then I also wanted to share the precalculated database (it doesn't seem logic to have everyone download it on their own).

I'm having a lot of problems, since they can read and access it but then when running > checkm data setRoot <checkm_data_dir> it generates a .dmanifest file per user, hence it tries to overwrite it each time a new user sets the path... could I have some input on what this file is doing? can I let everyone overwrite it? or maybe get my install version so everyone uses the same? does it ineed to be personalized?

thanks !

donovan-h-parks commented 2 years ago

Hi. The individual who setup the database end of CheckM has moved on to other ventures. I'm not that familiar with the exact role of the .dmanifest file. I think it should work so long as the path is staying the same. I'd certainly try testing it out first though. Alternatively, CheckM can be install system wide for all users. I think this is how most labs are using CheckM.

donovan-h-parks commented 2 years ago

Hi,

Starting with CheckM v1.1.6 the CHECKM_DATA_PATH environmental variable can be used to indicate the path to the CheckM reference data: https://github.com/Ecogenomics/CheckM/wiki/Installation#required-reference-data

Cheers, Donovan