Tag Archive for 'ubuntu'

Install PostgreSQL on Ubuntu 8.04

Published
by
Daz
on May 13, 2008
in linux, noteworthy and postgresql
. 17 Comments

Following up from my old guide to installing PostgreSQL (for Ubuntu 7.10), I thought i’d better do an update for the latest releases… :)

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.

Continue reading ‘Install PostgreSQL on Ubuntu 8.04’

Installing R/BioConductor on Ubuntu 8.04

Published
by
Daz
on May 7, 2008
in linux
. 1 Comment

The new version of Ubuntu is out, (as if you haven’t heard that by now), so that means a fresh install to play about with and working just the way I want! :D

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.

Installing VMware Tools on Ubuntu 8.04 (Hardy)

Published
by
Daz
on May 5, 2008
in linux, mac and snippets
. 0 Comments

If you’re a VMware user and want to play around with the latest version of Ubuntu in a VM (like me), you’ll need to get the vmware-tools installed. Unfortunately, things are not quite as straight forward as the previous release of Ubuntu yet, but it was a pretty easy thanks to this great guide.

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 …

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Bio-Linux - Bioinformatics Tools for Linux

Published
by
Daz
on March 7, 2008
in linux and noteworthy
. 2 Comments

Bio-Linux is a specialised Linux disro that provides both standard and cutting edge bioinformatics software tools on a Linux base.

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…

Continue reading ‘Bio-Linux - Bioinformatics Tools for Linux’

Install phpPgAdmin on Ubuntu 7.10

Published
by
Daz
on November 14, 2007
in linux and postgresql
. 9 Comments

Update: These instructions have been tested and work fine in the latest version of Ubuntu (8.04, Hardy Heron).

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.

  1. I am assuming here that you have set-up your PostgreSQL server using my set-up instructions and therefore have a password protected ‘postgres’ account and that logins require passwords. ↩

  2. Please make sure you have read the above footnote and understand the security implications of allowing this type of access to your database server - if you have not secured your administration accounts, do it now! ↩

Mount ISO Files With Nautilus

Published
by
Daz
on November 14, 2007
in linux
. 0 Comments

Here’s two short bash scripts that allow you to mount and unmount an ISO image easily within the right-click menu in Nautilus (the file manager in Gnome):

$ 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.

Installing Apache and PHP Troubles

Published
by
Daz
on November 13, 2007
in linux
. 0 Comments

I just recently set Apache up on my home server (more on the server at some point in the future), but I was having problems serving up php pages. Every time I tried to access a php based page, Firefox came up asking if I wanted to download a ‘.PHTML’ file!!! :(

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.

Install PostgreSQL on Ubuntu 7.10

Published
by
Daz
on November 5, 2007
in linux, noteworthy and postgresql
. 44 Comments

If you are using the latest version of Ubuntu (8.04 - Hardy Heron), you might find these slightly updated instructions useful.

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.

Continue reading ‘Install PostgreSQL on Ubuntu 7.10’

Installing VMware Tools on Ubuntu Gutsy

Published
by
Daz
on November 3, 2007
in linux and mac
. 3 Comments

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I’ve just started to play about with the new Ubuntu (7.10 - Gutsy), I have to say that I quite like it - I was a big fan of Feisty and all other Ubuntu releases previously, so this is more of the same good stuff.

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.