mirror essential tables from UCSC to a local mysql database. (change $ORG to mm8/hg18/dm3 or your organism of choice.)

ucsc.simple.sh

ORG=hg19
USER=brentp

# from: http://nsaunders.wordpress.com/2011/05/18/how-to-create-a-partial-ucsc-genome-mysql-database/

# create database
mysql -u $USER  -e "CREATE DATABASE $ORG";
mkdir -p ucsc-data/$ORG
cd ucsc-data/$ORG
for table in knownGene refGene ensGene kgXref chromInfo cpgIslandExt cytoBand
do
    mysql -u $USER $ORG -e "DROP TABLE $table;"
    # obtain table schema
    wget http://hgdownload.cse.ucsc.edu/goldenPath/$ORG/database/${table}.sql
    # create table
    mysql -u $USER $ORG < ${table}.sql
    # obtain and import table data
    wget http://hgdownload.cse.ucsc.edu/goldenPath/$ORG/database/${table}.txt.gz
    gunzip ${table}.txt.gz
    mysqlimport -u $USER --local $ORG ${table}.txt
done