kjolley / BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

Home Page:https://pubmlst.org/software/bigsdb/

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Database-specific configuration?

zmeel opened this issue · comments

commented

Hi Keith,

Currently I'm setting up our own BIGSdb but I struggle with database creation. I have created a sequence definition database and an isolate database according to the manual:

createdb Enterococcus_faecium_seqdef
psql -f seqdef.sql Enterococcus_faecium_seqdef

createdb Enterococcus_faecium_isolates
psql -f isolatedb.sql Enterococcus_faecium_isolates

I expected to find the configuration file (confix.xml) in /etc/bigsdb/dbases but nothing is there. Do I have to add this config.xml myself including all the other html files mentioned in the manual?

Thanks in advance!
Erik

You have to create the config.xml file yourself. There are basic examples in the xml directory.

Create config directories, e.g. /etc/bigsdb/dbases/enterococcus_faecium_seqdef and copy the seqdef_config.xml file to this (renaming it config.xml). Edit this file to use the name of the database you have created. Do similarly for the isolate database.

You don't need any of the HTML files - they're all optional used for site branding etc.

commented

Thanks! That was easy...