stars_setup.pl
Written by Keith Jolley
Copyright (c) 2004, University of Oxford
General
This Perl script will set up STARS for the first time for species supported by pubmlst.org. Template databases for these MLST schemes are automatically downloaded and set up for the user
Usage
stars_setup.pl [-s] [-c <dbase name>]
Options
stars_setup.pl has two command line options which can be combined:
- s - setup. Run with this option to set up your STARS environment. This creates a 'staden' directory in your home directory containing five sub-directories - 'failed','my_lists','new_data','renamed_traces' and 'session'.
- c <dbase name> - create. Use this to create a database with the name used. The script downloads a list of templates from pubmlst.org which it presents in a menu. Choose the species you're working on and a new database will be created in your PROJECTROOT directory (this will be created if necessary). Your startup script (.zshrc) will be modified to set this as your default database. Start a new shell for the changes in .zshrc to be available (or type 'source .zshrc' after running the script).
Templates available
These can be downloaded separately and modified for your own needs.
- NM-NEW-00: Neisseria spp.
- CJ-NEW-00: Campylobacter spp.
- CJMILLER-NEW-00: Campylobacter spp. (Miller primers)
- BCC-NEW-00: Burkholderia cepacia complex
If you work on a different organism and have developed your own template databases which you would like to make available on pubmlst.org, please contact us.