Hi,
I am wondering which databases are the explicitly needed data bases
for a new installation that isn't planning on using any of the UCSC
data.
For initial set up I used a combination of some blogs and Minimal
Browser Installation
http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation
I haven't seen a minimum required list of databases, although I've
gleaned that hgcentral is the only one that is absolutely required -
until now. (see below, I'm building to it)
I have been following this description for the genome DBs:
http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database
Interestingly, at no point in the "Building a new genome database"
process (
http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database)
is "giving readonly access to that database" mentioned. I will be
adding it to my automation script, which I hope to share as soon as
it's satisfactorily complete.
I checked the
ex.MySQLUserPerms.sh and note that:
#
# Read only access to genome databases for the browser CGI binaries
#
for DB in cb1 hgFixed hg17 proteins040315
do
${MYSQL} -e "GRANT SELECT, CREATE TEMPORARY TABLES on \
${DB}.* TO readonly@localhost IDENTIFIED BY 'access';" mysql
done
Note that I have none of the databases mentioned in the above stanza.
Also, there is no step within the "Building a new database" that
indicates that db users should be provided access to the new dbs in
order for them to be read. I think this needs addressing in the docs,
unless I'm missing something?
Now that I am at Step 13 of the "Building a new database" wiki, it
would seem that I also need a trackDB database.
The documentation is very clear on how to add multiple, different,
trackDB databases to the hg.conf, but it isn't very clear on why you
would be interested in doing that at all, nor at what stage in the
installation these databases are created. Also, which db users need
access to that/those databases?
So, the instructions for the creation of that database seem to be
missing, although there seems to be a couple of instructions on how to
add to that database, they are disparate and in some cases, different.
A single, clear, how to would be really useful.
Cheers
L.
------
I'm treading carefully
but it's the time of night
the snowy light
the subway roar
and the whispered fights
exciting sights
but it's not enough
I thought it was
I wish it was
I thought it was
-----
You name it - The Cannanes with Explosion Robinson.
https://youtu.be/MGrillKAzsI