# load chado_r3.2 postgres db
# plain postgres load 
# NOT using FlyBase-NG/ARGOS distribution of software (see below for that)
# 20May04

# if need be start postgres -- see postgres docs
# set shell env and path for postgres command line use -- see postgres docs
# the value $POSTGRES_HOME should be in your shell environ
# check postgres db contents - this should work for you
psql -l

# load in new chado postgres dump - change dbname/note as needed
# find names from ftp directories below
set dbname=chado_r3.2_18
set dbnote='flybase annot. r3.2 8Mar04'

# put data dump somewhere temporarily to load ...
cd /var/tmp/

ncftpls ftp://flybase.net/genomes/Drosophila_melanogaster/current/pgsql/
ncftpget ftp://flybase.net/genomes/Drosophila_melanogaster/current/pgsql/$dbname.gz

# -- OR -- look for possibly newer/older versions in
ncftpls ftp://flybase.net/genomes/Drosophila_melanogaster/
# e.g. Drosophila_melanogaster/dmel_r3.2.0_05142004/pgsql/chado_r3.2_25.gz

# create pg chado database at standard postgres storage location
createdb $dbname "$dbnote"

# this addition of language may not be needed (was with earlier releases)
createlang -d $dbname plpgsql

# load in data -- it probably takes an hour or more here.
(zcat $dbname.gz | psql -d $dbname -f - )>&  log.chload &

# check place where data is stored -- new chado db should be here now
du $POSTGRES_HOME/data/base/

# final step to clean up, make db as speedy as possible
vacuumdb -d $dbname --full --analyze --echo


#---------------------------------------------------
# load chado_r3.2 postgres db
# using FlyBase-NG/ARGOS distribution of software
# 10mar04

# FLYBASE_PGDATA should be defined in argos configs ..
# see below, Env key FB_PGDATA changed to FLYBASE_PGDATA

# set $ARGOS_ROOT and env variables
cd /path/to/argos
source `ROOT/bin/argos-env`

# if need be start postgres
$ARGOS_ROOT/ROOT/bin/run-postgres2 start

# set shell env and path for postgres command line use
source `$ARGOS_ROOT/ROOT/bin/run-postgres2 setenv`

# check data location is defined as $ARGOS_ROOT/flybase/indices/pgsql
env | grep FLYBASE_PGDATA

# check postgres db contents
psql -l

# load in new chado postgres dump
set dbname=chado_r3.2_19
set dbnote='flybase annot. r3.2 16Mar04'

# put data dump somewhere ...
cd $ARGOS_ROOT/flybase/tmp/
rsync rsync://flybase.net/flybaseftp/genomes/Drosophila_melanogaster/current/pgsql/$dbname.gz . -au &

# put pg data indices into pre-defined location
# FLYBASE_PGDATA =  $ARGOS_ROOT/flybase/indices/pgsql
createdb --location=FLYBASE_PGDATA $dbname "$dbnote"

createlang -d $dbname plpgsql

# load in data
(zcat $dbname.gz | psql -d $dbname -f - )>&  log.chload &

# check place where data is stored
du $ARGOS_ROOT/flybase/indices/pgsql

# final step to clean up, make db as speedy as possible
vacuumdb -d $dbname --full --analyze --echo