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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
128 stars 33 forks source link

Documentation does not say how to download databases #40

Closed mw55309 closed 4 years ago

mw55309 commented 4 years ago

Hello

Section https://github.com/biobakery/phylophlan/wiki#databases says "PhyloPhlAn 3.0 is able to automatically download two databases of universal markers for prokaryotes:" but does not then go on to say how phylophlan does this, or what commands a user needs to execute to download those databases.

When installing from conda, no databases come with the install:

phylophlan --database_list --diversity low
Available databases in "phylophlan_databases/":
fasnicar commented 4 years ago

Hello Mick, Thanks for trying PhyloPhlAn. The two available databases are phylophlan and amphora2 and are automatically downloaded only when running PhyloPhlAn. That's why you don't see and database right after the installation.

We can definitely make this more clear from the documentation.

Many thanks, Francesco

mw55309 commented 4 years ago

Great, thank you 👍