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Updating_database.md

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Last updated

28th March 2025

IMPORTANT:

Updating the MLST database DOES NOT update the values in the dropdown menu in the MLST tool. We need to modify the values in the dropdown menu.

Procedure followed

Here is the document/manual I followed to update the DB https://github.com/tseemann/mlst?tab=readme-ov-file#updating-the-database

Login to VIGASP-Galaxy VM.

# Location of the DB
/opt/galaxy/21.09/database/dependencies/_conda/envs/__mlst@2.16.1/db

# Script to download
/opt/galaxy/21.09/database/dependencies/_conda/envs/__mlst@2.16.1/scripts

# Go into the scripts folder (you need to have write access!)
% cd /home/user/sw/mlst/scripts

# Run the downloader script (you need 'wget' installed)
% ./mlst-download_pub_mlst | bash

# Save the old database folder
% mv ../db/pubmlst ../db/pubmlst.old

# Put the new folder there
% mv ./pubmlst ../db/

# Regenerate the BLAST database
% ./mlst-make_blast_db

# Check schemes are installed
% ../bin/mlst --list

Note:

# Here is the New DB
/opt/galaxy/21.09/database/dependencies/_conda/envs/__mlst@2.16.1/db/pubmlst

Updated DB contains two schemes for Ecoli (ecoli and ecoli_4) Ecoli4 corresponds to Achtman Ecoli corresponds to Pasteur