xwu

USE caliban;
LOAD DATA LOCAL INFILE '~/morbidmap.txt' INTO TABLE `morbidmap` FIELDS TERMINATED BY '|' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE '~/omim.tsv' INTO TABLE `omim` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE '~/refFlat.txt' INTO TABLE `refflat` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n' IGNORE 1 LINES;
LOAD DATA LOCAL INFILE '~/snpedia.tsv' INTO TABLE `snpedia` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';

USE dbsnp;
LOAD DATA LOCAL INFILE '~/OmimVarLocusIdSNP.bcp' INTO TABLE `OmimVarLocusIdSNP` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE '~/b129_SNPChrPosOnRef_36_3.bcp' INTO TABLE `b129_SNPChrPosOnRef_36_3` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';

xwu

CREATE DATABASE `ariel` DEFAULT CHARACTER SET ASCII COLLATE ascii_general_ci;
CREATE DATABASE `caliban` DEFAULT CHARACTER SET ASCII COLLATE ascii_general_ci;
CREATE DATABASE `dbsnp` DEFAULT CHARACTER SET ascii COLLATE ascii_general_ci;

CREATE USER 'reader'@'localhost' IDENTIFIED BY 'shakespeare';
GRANT SELECT ON *.* TO `reader`@'localhost';
CREATE USER 'reader'@'%' IDENTIFIED BY 'shakespeare';
GRANT SELECT ON *.* TO `reader`@'%';

CREATE USER 'updater'@'localhost' IDENTIFIED BY 'shakespeare';

xwu

sudo apt-get install wget
sudo apt-get install zip unzip

sudo apt-get install apache2
sudo apt-get install apache2-threaded-dev

cd /etc/apache2/mods-enabled
sudo ln -s /etc/apache2/mods-available/expires.load expires.load
sudo ln -s /etc/apache2/mods-available/deflate.load deflate.load
sudo ln -s /etc/apache2/mods-available/rewrite.load rewrite.load

xwu

sudo mkdir /var/trait
sudo wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit -O /var/trait/hg18.2bit

cd

# dbSNP (only two tables)
wget ftp://ftp.ncbi.nih.gov:21/snp/organisms/human_9606/database/organism_data/OmimVarLocusIdSNP.bcp.gz
wget ftp://ftp.ncbi.nih.gov:21/snp/organisms/human_9606/database/organism_data/b129/b129_SNPChrPosOnRef_36_3.bcp.gz
gunzip OmimVarLocusIdSNP.bcp.gz
gunzip b129_SNPChrPosOnRef_36_3.bcp.gz

xwu

cd
wget http://github.com/xwu/trait-o-matic/tarball/master -O trait.tar.gz
rm -Rf xwu-trait-o-matic-*
tar -zxvf trait.tar.gz
sudo rm -Rf /usr/share/trait
sudo cp -R xwu-trait-o-matic-*/core /usr/share/trait

cd /usr/share/trait
sudo python setup.py build_ext --inplace