useradd syntax

useradd [options] {username}

Useful options are:

-d

declare the users home directory

-m

force ‘useradd’ to create the home directory

-D

accept the system defaults for account settings

An alternative for ‘useradd’ though is ‘adduser’:

adduser {username}

This will then prompt you for all the information needed to set up the account.

making the user an administrator (with sudo)

As the root user…

visudo

Then underneath the entry for ‘root’ just add in an entry with the desired user name:

{username} ALL=(ALL) ALL

I’ve seen things like this posted on the net before but never really had a chance to play with the idea. But as I’m now using git and svn a lot more these days (fingers crossed i’ll be totally free of cvs soon!) I thought it was about time I pulled my finger out.

So here’s the end goal, in a normal directory, we just get a normal bash promt, but in a directory controlled by git or svn, we also get an addition telling us the source control tool in use and the current branch:

So, fire up yer terminal and add the following to your .profile, .bash_profile or .bashrc (whichever one you use):

parse_git_branch () {
	git name-rev HEAD 2> /dev/null | sed 's#HEAD\ \(.*\)# (git::\1)#'
}
parse_svn_branch() {
	parse_svn_url | sed -e 's#^'"$(parse_svn_repository_root)"'##g' | awk '{print " (svn::"$1")" }'
}
parse_svn_url() {
	svn info 2>/dev/null | sed -ne 's#^URL: ##p'
}
parse_svn_repository_root() {
	svn info 2>/dev/null | sed -ne 's#^Repository Root: ##p'
}
 
BLACK="\[\033[0;38m\]"
RED="\[\033[0;31m\]"
RED_BOLD="\[\033[01;31m\]"
BLUE="\[\033[01;34m\]"
GREEN="\[\033[0;32m\]"
 
export PS1="$BLACK[ \u@$RED\h $GREEN\w$RED_BOLD\$(parse_git_branch)\$(parse_svn_branch)$BLACK ] "

Simples. Now just open up a new terminal and move into a project directory using svn or git.

QGtkStyle made it’s way into the Qt snapshots this week, meaning it will become part of the Qt 4.5 release. Technical users can already compile and use it on their own desktop, but once Qt 4.5 is out it will simply replace Cleanlooks as the default application style Qt uses on GNOME desktops.

via

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 …

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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

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.

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.

read more

The first thing we will do is generate a key for the SHH version 1 protocol (just in case you are connecting to an older machine):

ssh-keygen -t rsa1

SSH-Keygen will respond with something like the following:

Generating public/private rsa1 key pair.
Enter file in which to save the key (/Users/daz/.ssh/identity):

At this point hit enter then you will be prompted for a passphrase - this is a form of password that will be used to generate your unique keys and can contain any set of characters and spaces - something like "I’m really liking all of this geeky nonsense!" is a perfectly acceptable passphrase - just whatever you do, don’t use an empty passphrase. After entering (and confirming) your passphrase you will get the following output:

Your identification has been saved in /Users/daz/.ssh/identity.
Your public key has been saved in /Users/daz/.ssh/identity.pub.

This means that our identity keys have been generated. Now we just need to create a pair of keys for the SSH2 protocol - you can use the same or different passphrases for these keys - it’s up to you…

ssh-keygen -t dsa

Then

ssh-keygen -t rsa

You should now have three sets of keys in your ~/.ssh directory, the ones with the .pub extension are your public keys (what we need to put on your other machines) and the others are your private keys - these must be kept safe!

So, let’s use scp to copy the files across:

scp ~/.ssh/*.pub daz@MyServer:/home/daz/

Then log into your server using ssh and issue the following commands:

cat identity.pub >>~/.ssh/authorized_keys
cat id_dsa.pub >>~/.ssh/authorized_keys
cat id_rsa.pub >>~/.ssh/authorized_keys
rm identity.pub id_dsa.pub id_rsa.pub

This populates the authorized_keys file on our server with the three public keys that we have just transferred and then removes them as they’re no longer needed here.

That’s everything done, now all we have to do is log out of our server, and then try and log back in via ssh - a password should no longer be required!¹