This quick walk-through are my notes for installing the PostgreSQL database server and the PgAdmin administration application on Ubuntu Linux, and also set up the server so it allows access to other PC’s on your network.

Before we move on, this guide was tested on the current release of Ubuntu Linux, (8.04 - Hardy Heron) and PostgreSQL 8.3, but it should also be applicable to older versions (of Ubuntu and PostgreSQL) and other Debian based distros.

Right for the basic installation, at the command-line, enter the following commands (or search for the listed packages in synaptic if you prefer that way of working):

$ sudo apt-get install postgresql postgresql-client postgresql-contrib
$ sudo apt-get install pgadmin3

This installs the database server/client, some extra utility scripts and the pgAdmin GUI application for working with the database.

Now we need to reset the password for the ‘postgres’ admin account for the server, so we can use this for all of the system administration tasks. Type the following at the command-line (substitute in the password you want to use for your administrator account):

$ sudo su postgres -c psql template1
template1=# ALTER USER postgres WITH PASSWORD 'password';
template1=# \q

That alters the password for within the database, now we need to do the same for the unix user ‘postgres’:

$ sudo passwd -d postgres
$ sudo su postgres -c passwd

Now enter the same password that you used previously.

Then, from here on in we can use both pgAdmin and command-line access (as the postgres user) to run the database server. But before you jump into pgAdmin we should set-up the PostgreSQL admin pack that enables better logging and monitoring within pgAdmin. Run the following at the command-line:

$ sudo su postgres -c psql < /usr/share/postgresql/8.3/contrib/adminpack.sql

Finally, we need to open up the server so that we can access and use it remotely - unless you only want to access the database on the local machine. To do this, first, we need to edit the postgresql.conf file:

$ sudo gedit /etc/postgresql/8.3/main/postgresql.conf

Now, to edit a couple of lines in the ‘Connections and Authentication’ section…

Change the line:

#listen_addresses = 'localhost'

to

listen_addresses = '*'

and also change the line:

#password_encryption = on

to

password_encryption = on

Then save the file and close gedit.

Now for the final step, we must define who can access the server. This is all done using the pg_hba.conf file.¹

$ sudo gedit /etc/postgresql/8.3/main/pg_hba.conf

Comment out, or delete the current contents of the file, then add this text to the bottom of the file:

# DO NOT DISABLE!
# If you change this first entry you will need to make sure that the
# database
# super user can access the database using some other method.
# Noninteractive
# access to all databases is required during automatic maintenance
# (autovacuum, daily cronjob, replication, and similar tasks).
#
# Database administrative login by UNIX sockets
local   all         postgres                          ident sameuser
# TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD

# "local" is for Unix domain socket connections only
local   all         all                               md5
# IPv4 local connections:
host    all         all         127.0.0.1/32          md5
# IPv6 local connections:
host    all         all         ::1/128               md5

# Connections for all PCs on the subnet
#
# TYPE DATABASE USER IP-ADDRESS IP-MASK METHOD
host    all         all         [ip address]          [subnet mask]  md5

and in the last line, add in your subnet mask (i.e. 255.255.255.0) and the IP address of the machine that you would like to access your server (i.e. 138.250.192.115). However, if you would like to enable access to a range of IP addresses, just substitute the last number for a zero and all machines within that range will be allowed access (i.e. 138.250.192.0 would allow all machines with an IP address 138.250.192.x to use the database server).

That’s it, now all you have to do is restart the server:

$ sudo /etc/init.d/postgresql-8.3 restart

And all should be working.

One of the tools that I currently need (for the thesis work) is R and the BioConductor libraries. So here’s a quick run down on getting them up and installed on Hardy…

First up, run these commands in a terminal:

sudo apt-get install build-essential g77 gfortran
sudo apt-get install refblas3 refblas3-dev zlib1g-dev
sudo apt-get install r-base

This will then install the R base packages and some of the BioConductor packages, along with the gcc and fortran compilers and some other libraries that will be required for the next step.

sudo -s
R

Now at the R prompt, type the following…

source("http://www.bioconductor.org/biocLite.R")
biocLite()

Now sit back for a few minutes while your system configures BioConductor for you.

The latest version of Ubuntu (8.04 a.k.a. Ubuntu Hardy - the world’s most popular Linux distribution) came out yesterday on April 24th. I downloaded it right away to play with on VMware Fusion, my Mac virtualization tool of choice (though I’ve now been told this works in VMware Workstation and VMware Player on the PC too!). It worked pretty well out of the box, with even seamless mouse support working right away, but I needed, of course, to install VMware Tools too, as any good VMware user would do. From there, things turned sour, and I was bombarded with error messages …

read more

I wrote a post on my old blog a little while back now detailing how to use the packages from Bio-Linux in Ubuntu Linux, but it got missed in the migration (sorry to all those who have been searching for it). Here’s a repost and update for Ubuntu 7.10…

Log into your system and open up a terminal, then follow these steps…

sudo gedit /etc/apt/sources.list

Add the following lines to the end of the file:

# Bio-Linux package repository
deb http://envgen.nox.ac.uk/bio-linux/ unstable bio-linux

Save and close the file, now back at the terminal type the following:¹

sudo apt-get update
sudo apt-get install bio-linux-base-directories bio-linux-staden

Next step is to set-up your environment for Bio-Linux…

sudo gedit /etc/bash.bashrc

Add the following lines to the end of the file:

# Set up Bio-Linux Environment
source /usr/local/bioinf/config_files/aliasrc
source /usr/local/bioinf/config_files/bioenvrc

Save and close the file.

That’s it, now all of the packages available through Bio-Linux are now available to you in Ubuntu. One final word of warning… I’ve noticed that a few of the packages are a little out of date, (the Bio-Linux version of Taverna is 1.4, but 1.7 is now available)² so it might be worth checking the version numbers before installing things.

phpPgAdmin is a web based GUI for administrating a PostgreSQL database server.

Here’s some quick notes on getting it installed easily on Ubuntu 7.10…

In the terminal enter the following:

$ sudo apt-get install phppgadmin

This will set up and install all of the phpPgAdmin packages. It will also set-up and configure Apache and php5 for you too if you haven’t installed these already.

Next we need to create a symlink to phpPgAdmin so that Apache can find it:

$ sudo ln -s /etc/phppgadmin/apache.conf /etc/apache2/conf.d/phppgadmin.conf

Now if you navigate to http://localhost/phppgadmin you should be greeted with the phpPgAdmin screen. If your user account has a PostgreSQL account however, you will be logged in automagically.

Optionally, if you would like to be able to use the phpPgAdmin interface as the default ‘postgres’ administration account,¹ you will need to do the following²…

$ sudo gedit /usr/share/phppgadmin/conf/config.inc.php

Now find and change the following line

$conf['extra_login_security'] = true;

to

$conf['extra_login_security'] = false;

Save and close gedit. Now all you need to do is restart Apache.

$ sudo /etc/init.d/apache2 reload

Now if you head on over to http://localhost/phppgadmin all should be ready for you.

$ sudo mkdir /media/ISO
$ cd ~/.gnome2/nautilus-scripts/
$ gedit "Mount ISO Image"

Now paste this code into the file:

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#!/bin/bash
#
for I in `echo $*`
do
foo=`gksudo -u root -k -m "enter your password for root terminal access" /bin/echo "got r00t?"`
sudo mount -o loop -t iso9660 $I /media/ISO
done
done
exit0

Save, and exit gedit.

$ gedit "Unmount ISO Image"

Then paste this code in this file:

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#!/bin/bash
#
for I in `echo $*`
do
foo=`gksudo -u root -k -m "enter your password for root terminal access" /bin/echo "got r00t?"`
sudo umount $I
done
done
exit0

Save, and exit gedit. Now finally…

$ chmod a+x *

Now you can mount and unmount ISO files by using the ‘Scripts’ options in the right-click menu.

Thanks to the Ubuntu Blog for the information.

Thankfully the answer (like most things with Ubuntu) was found on the Ubuntu Forums…

Simply edit the file /etc/apache2/apache2.conf by adding the following line:

AddType application/x-httpd-php .php .phtml

Now php files should be handled by the server in the way that they were intended.

This quick walk-through are my notes for installing the PostgreSQL database server and the PgAdmin administration application on Ubuntu Linux, and also set up the server so it allows access to other PC’s on your network.

Before we move on, this guide was tested on the current release of Ubuntu Linux, (7.10 - Gutsy Gibbon) and PostgreSQL 8.2, but it should also be applicable to older versions (of Ubuntu and PostgreSQL) and other Debian based distros.

Right for the basic installation, at the command-line, enter the following commands (or search for the listed packages in synaptic if you prefer that way of working):

$ sudo apt-get install postgresql postgresql-client postgresql-contrib
$ sudo apt-get install pgadmin3

This installs the database server/client, some extra utility scripts and the pgAdmin GUI application for working with the database.

Now we need to reset the password for the ‘postgres’ admin account for the server, so we can use this for all of the system administration tasks. Type the following at the command-line (substitute in the password you want to use for your administrator account):

$ sudo su postgres -c psql template1
template1=# ALTER USER postgres WITH PASSWORD 'password';
template1=# \q

That alters the password for within the database, now we need to do the same for the unix user ‘postgres’:

$ sudo passwd -d postgres
$ sudo su postgres -c passwd

Now enter the same password that you used previously.

Then, from here on in we can use both pgAdmin and command-line access (as the postgres user) to run the database server. But before you jump into pgAdmin we should set-up the PostgreSQL admin pack that enables better logging and monitoring within pgAdmin. Run the following at the command-line:

$ sudo su postgres -c psql < /usr/share/postgresql/8.2/contrib/adminpack.sql

Finally, we need to open up the server so that we can access and use it remotely - unless you only want to access the database on the local machine. To do this, first, we need to edit the postgresql.conf file:

$ sudo gedit /etc/postgresql/8.2/main/postgresql.conf

Now, to edit a couple of lines in the ‘Connections and Authentication’ section…

Change the line:

#listen_addresses = 'localhost'

to

listen_addresses = '*'

and also change the line:

#password_encryption = on

to

password_encryption = on

Then save the file and close gedit.

Now for the final step, we must define who can access the server. This is all done using the pg_hba.conf file.¹

$ sudo gedit /etc/postgresql/8.2/main/pg_hba.conf

Comment out, or delete the current contents of the file, then add this text to the bottom of the file:

# DO NOT DISABLE!


If you change this first entry you will need to make sure that the

database

super user can access the database using some other method.

Noninteractive

access to all databases is required during automatic maintenance

(autovacuum, daily cronjob, replication, and similar tasks).

#

Database administrative login by UNIX sockets

local   all         postgres                          ident sameuser

TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD

"local" is for Unix domain socket connections only

local   all         all                               md5

IPv4 local connections:

host    all         all         127.0.0.1/32          md5

IPv6 local connections:

host    all         all         ::1/128               md5

Connections for all PCs on the subnet

#

TYPE DATABASE USER IP-ADDRESS IP-MASK METHOD

host    all         all         [ip address]          [subnet mask]  md5

and in the last line, add in your subnet mask (i.e. 255.255.255.0) and the IP address of the machine that you would like to access your server (i.e. 138.250.192.115). However, if you would like to enable access to a range of IP addresses, just substitute the last number for a zero and all machines within that range will be allowed access (i.e. 138.250.192.0 would allow all machines with an IP address 138.250.192.x to use the database server).

That’s it, now all you have to do is restart the server:

$ sudo /etc/init.d/postgresql-8.2 restart

And all should be working.

As I’m working with VMWare Fusion, the first thing that needs to be done is install the VMWare Tools. This is quite simply done with the following lines in the terminal once you have started your VM and mounted the tools image (Virtual Machine > Install VMWare Tools in the menu):

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sudo aptitude update
sudo aptitude install build-essential linux-headers-$(uname -r)
cp -a /media/cdrom/VMwareTools* /tmp/
cd /tmp/
tar -vxzf VMwareTools*.gz
cd vmware-tools-distrib/
sudo ./vmware-install.pl

The just accept all of the defaults for the installation package.

Cheers to Ubuntu Tutorials for the info.