GeezerVison

Note that if you intend to use the BioJavaX/ Hibernate bindings to BioSQL you should refer instead to the BioJavaX documentation.

by David Huen

This document describes how to install and use BioSQL. BioSQL is a part of the OBDA standard and was developed as a common sequence database schema for the different language projects within the Open Bioinformatics Foundation.

While BioSQL is fairly vendor-neutral in its design, this tutorial is based on the case that I know best, that is, the installation of BioSQL on an x86 machine running RedHat 7.2.

Installing Postgresql

If not already installed, PostgreSQL can be installed from RPMs with:

rpm -ivh postgresql-7.2.1-5.i386.rpm postgresql-libs-7.2.1-5.i386.rpm postgresql-server-7.2.1-5.i386.rpm

Root privileges will almost certainly be required (if not your machine is seriously insecure!!!). You will also need a JDBC to permit Java to connect to your PostgreSQL database and that can be installed with postgresql-jdbc-7.1.3-2.i386.rpm. However, I would recommend downloading the latest from here. You will end up with a jar file containing the JDBC implementation which you will need to place in your CLASSPATH.

The installs will place a control script within /etc/init.d<code> named <code>postgresql. When this script runs for the first time, it will create a database cluster and initialise it. This cluster is the set of files used by the database for storage purposes.

On RH7.2 the default location for the cluster in at /var/lib/pgsql/. This is a bit of a disadvantage as /var is usually a pretty small partition. It is possible at this stage to symlink /var/lib/pgsql to a directory within another partition altogether to circumvent this problem. I would suggest doing this immediately.

At this stage, you will need to create the database you intend using and a user to use it. I would suggest not using the superuser named postgres for anything other than occasional essential administration.

At this point, I will digress briefly into PostgreSQL authentication as choices you make will affect what you can do. PostgreSQL has a variety of routes to achieve this. The default at installation permits connection only from local users and permits access to a database only by a user of the same username. This may be quite adequate for experimentation but not so convenient if you want to set up a BioSQL database for several local users or possibly even remote users.

PostgresQL has other mechanisms which are described in their documentation. Authentication is specifically described here. You might consider password authentication but do use md5 encryption with this option, especially if you intend to authenticate remote users. In the Redhat 7.2 installation, the file you will need to edit to set these options is /var/lib/pgsql/data/pg_hba.conf. The location of this file varies with other distributions.

As initially installed in RH7.2, PostgreSQL will require root privileges to set up further. The postgres superuser cannot be logged into but you can invoke the necessary commands from root to execute:

$ su postgres -c 'createdb <insert db name here>'

and a user created with:

$ su postgres -c 'createuser <insert user name here>'

For the purposes of this tutorial, I will not change the default authentication so the database name should be chosen to correspond to your user name. The user name used in this exercise is gadfly and this will be reflected in the choice of database name and user name. One additional change that will be necessary is to enable TCP/IP connections as the Unix domain socket restriction of the default installation is incompatible with the PostgreSQL JDBC implementation.

To do so, you need to add the -i flag to the startup script. Edit /etc/init.d/postgresql and change the line

su -l postgres -s /bin/sh -c "/usr/bin/pg_ctl -D $PGDATA -p /usr/bin/postmaster start  > /dev/null 2>&1" < /dev/null

to

su -l postgres -s /bin/sh -c "/usr/bin/pg_ctl -o "-i" -D $PGDATA -p /usr/bin/postmaster start  > /dev/null 2>&1" < /dev/null

The /var/lib/pgsql/data/pg_hba.conf file will also need to be edited to permit access via TCP/IP. This can be achieved by uncommenting:

#host       all         127.0.0.1     255.255.255.255    trust

Both these operations require root access: seek advice as to the best option given your local security circumstances.

One additional change is that postgresql in RH7.3 does not come with the pgsql language enabled. As BioSQL uses that for acceleration, you will need to enable it. This can be done within root with:

su postgres -c 'createlang plpgsql template1'

Installing BioSQL

The PostgreSQL server must be running to complete the BioSQL installation. You can check that it is with:

$ /etc/rc.d/postgresql status

and doing:

$ /etc/rc.d/postgresql start

if it is not running. You may require root privileges for this. You should have PostgreSQL started up during system startup with the SysV init system that comes with most Unixen.

You will need three scripts that serve to initialise the new database with the BioSQL schema and load accelerators for this schema. These are:

biosql-accelerators-pg.sql
biosqldb-assembly-pg.sql
biosqldb-pg.sql

They may be obtained from here.

We now need to load the schema into the database we have created. We do so as follows (user entries are prefixed by $ or gadfly==>):

$ psql gadfly
Welcome to psql, the PostgreSQL interactive terminal.

Type:  \copyright for distribution terms
       \h for help with SQL commands
       \? for help on internal slash commands
       \g or terminate with semicolon to execute query
       \q to quit
gadfly=> \i biosqldb-pg.sql
CREATE
psql:biosqldb-pg.sql:13: NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index 'biodatabase_pkey' for table 'biodatabase'
CREATE
<rest of output snipped>
INSERT 16862 1
psql:biosqldb-pg.sql:304: NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index 'cache_corba_support_pkey' for table 'cache_corba_support'
CREATE
gadfly=> \i biosqldb-assembly-pg.sql
<rest of output snipped>
gadfly=> \i biosql-accelerators-pg.sql
<rest of output snipped>
gadfly=> \q

$

Let’s walk through the session above. psql is the name of the PostgreSQL interactive shell. We invoke it to connect to the PostgreSQL server and accept commands for a database named gadfly that we had created earlier. psql starts and displays its user prompt. All psql commands begin with a backslash (\). The \i instructs psql to take input from a file. I instruct psql to take input from the biosqldb-pg.sql, biosqldb-assembly-pg.sql and biosql-accelerators-pg.sql successively. psql reads the SQL statements within each of the files and proceeds to construct the BioSQL database schema, printing out a summary of its actions as it proceeds. Finally, I quit the psql interactive shell with \q. At this point you have a BioSQL schema installed and ready to run!!!

Do remember that if you do not explicitly load the JDBC drivers in your code, you should set a Java environment variable to tell it what to look for like so:

java -Djdbc.drivers=org.postgresql.Driver <whatever your java code is>

NOTE: If you are using the 1.3 version of Biojava with the Singapore schema, do not install biosqldb-assembly-pg.sql or biosql-accelerators-pg.sql as described above. All you will need is the the new biosqldb-pg.sql. There appear to be performance issues in some cases when the other stuff is installed also. This note will be updated eventually to reflect this advice.