search

tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
831 stars 226 forks source link

How to update HMM databases #171

Open tseemann opened 8 years ago

tseemann commented 8 years ago

Bart Ailey wrote:

The documentation is good but I could not find out how to update the default databases it runs on. Especially the HMM databases. I read about the adding the databases and found the relevant scripts:

ll total 100K -rwxrwxr-x 1 500 500 52K Feb 14 2015 prokka -rwxrwxr-x 1 500 500 3.5K Feb 14 2015 prokka-biocyc_to_fasta_db -rwxrwxr-x 1 500 500 1015 Feb 14 2015 prokka-build_kingdom_dbs -rwxrwxr-x 1 500 500 3.7K Feb 14 2015 prokka-cdd_to_hmm -rwxrwxr-x 1 500 500 3.1K Feb 14 2015 prokka-clusters_to_hmm -rwxrwxr-x 1 500 500 4.7K Feb 14 2015 prokka-genbank_to_fasta_db -rwxrwxr-x 1 500 500 2.9K Feb 14 2015 prokka-genpept_to_fasta_db -rwxrwxr-x 1 500 500 4.2K Feb 14 2015 prokka-hamap_to_hmm -rwxrwxr-x 1 500 500 1.2K Feb 14 2015 prokka-make_tarball -rwxrwxr-x 1 500 500 2.7K Feb 14 2015 prokka-tigrfams_to_hmm -rwxrwxr-x 1 500 500 3.7K Feb 14 2015 prokka-uniprot_to_fasta_db

But how would you use them to update the files the db directory?

skDooley commented 5 years ago

I am trying to find the same thing. Is there an answer to this?