Archive for the 'linux' Category

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
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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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Unix Toolbox

Published
by
Daz
on March 23, 2008
in linux, mac and snippets
. 0 Comments

Found this via a post on Digg. A very useful read if you want to get some more advanced things done in Unix.

This document is a collection of Unix/Linux/BSD commands and tasks which are useful for IT work or for advanced users. This is a practical guide with concise explanations, however the reader is supposed to know what s/he is doing.

full article

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’

Stephen Fry on the Eee PC

Published
by
Daz
on February 4, 2008
in linux and snippets
. 0 Comments

I really like the Eee PC - some people at work here have them, and if I could get it past the wife, i’d happily have one! ;)

Seems like the well spoken geek Stephen Fry is quite a fan too:

I am writing this article on a kind of mini John the Baptist, a system that prepares the way of the software saviour whose coming will deliver the 90% of world computer users who suffer under Windows from the expensive, clumsy, costly, ugly, pricey toils of Microsoft.

The Asus EEE PC perched on my knee combines GNU software with a Linux kernel powered by an Intel Celeron Mobile Processor to produce a very extraordinary little laptop. It weighs less than a kilogram, starts up from cold in about 12 seconds and shuts down in five. It has no internal hard disk and no CD drive. It offers 512MB of RAM, 4GB of storage and a seven-inch display; wireless, dial-out modem and ethernet adaptors are available for networking and internet connections, three USB ports, mini-jack sockets for headphones and microphone, a VGA out, an SD card slot and a built-in webcam. All for about £200 - less than the price of a show, dinner and taxi for two in London’s West End.

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SSH Shared-Key Setup - SSH Logins Without Passwords

Published
by
Daz
on January 10, 2008
in linux and mac
. 0 Comments

SSH is a great tool for remotely accessing another machine, but entering your password every time you log into a remote box can be a pain if you would like to set-up some background scripts to connect to a server and do something (i.e. a backup script running as a cron job). Here’s how I set-up my Mac to be able to log into my server without the need for a password to be entered each time - the instructions should be good for any variant of Unix/Linux, but you need to take into account path names etc. on your machine.

Continue reading ‘SSH Shared-Key Setup - SSH Logins Without Passwords’

Getting Your DVDs Onto Your Mac/iPod/iPhone

Published
by
Daz
on December 29, 2007
in linux, mac and snippets
. 0 Comments

I’d looked at Handbrake a while back but the GUI was far too confusing for a simpleton like me. It seems like it’s been cleaned up quite a bit now and looks rather useful! (The little video giving an overview of how to work things helps too!)

Handbrake is one of those applications that we adore here at TUAW HQ. It makes converting DVDs into a variety of digital files a snap (though only use it with DVDs you own. Don’t be pirates, kids). Chris Breen, of Macworld fame (and an amateur astronomer it would seem) shows us how to use HandBrake like a pro. Breen goes a step beyond ‘use the presets’ and delves into what many of the options HandBrake offers up actually do, and how they impact your files.

via

Darwin Calendar Server

Published
by
Daz
on November 29, 2007
in linux, mac and snippets
. 0 Comments

At the moment I’m a very happy user of Google calendar and Spanning Sync for all my scheduling needs. But the geek in me fancies playing about with things so I’m thinking about setting up a CalDav server (when time permits) so Cat and I can organise our lives accordingly.

Here’s some pages I’ve been reading whilst doing my research.

Will possibly post more as and when I get a chance to play about with things…

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! ↩