Upgrading from Ubuntu 12.10 to 13.04 Raring Ringtail

It is April and Ubuntu 13.04 named Raring Ringtail has just been released a couple of days ago. Should you switch from an old version, or use it as an alternative to Windows 7? Well, that depends on your situation. Although the Raring Ringtail has a few new features, most of this is under the hood, and most differences between 12.10 and 13.04 are not noticeable immediately. It is also important to note that this version is only supported for 9 months from now, which means you will have to update again when 13.10 comes out. The alternative is to stay with 12.04 LTS, the long term support of 5 years.

Well, I cannot not install the latest version, because I am just too curious to see what the latest buzz is about, so this is how I updated from 12.10 to 13.04 on my Dell Inspiron 14z.

I took the following preparations in case something goes horribly wrong.

• Manual backup of my files onto an external hard drive.
• Sync all files with dropbox.
• Make a backup file with Deja Dup of the Home folder.
• Get a list of all installed software with :
• dpkg --get-selections > installed-software
• Make a bootable USB stick of 13.04 as a plan B.
• Export boomarks in firefox.

To update the system, I choose to use the software updater. I had not used it previously when updating from 12.04 LTS to 12.10, but thought I would try this time. As rumor online has it that using a clean install gives a better outcome, I prepared the bootable USB stick, but still wanted to go ahead with the software updater. It took about 1 hour to download all packages (crappy internet connection),  and another 30 minutes to update everything and purge the system of old packages. After a restart, everything was updated, although so far I have not noticed any great changes, neither in speed (it was really fast before anyway) nor in appearance (a bit different, but pretty much the same).

How to turn off the Amazon search in the dash

The latest distribution of Ubuntu (12.10, Quantal Quetzal) has an improved search function, which by default includes searching Amazon. This can be very handy if you like Amazon, but it also raises concerns for privacy. The issue is hot topic in the Ubuntu community, with some saying, that it's a good source of revenue for the Canonical, the Ubuntu developers, but other's being concerned about the commercialisation of a open source operating system.
I think having Amazon included is a interesting option, but I do think, that it should not be default, but rather optional, maybe it could be included in the installation menu, when you set keyboard option, time zone, etc.
Also, Ubuntu is a international project, people from all over the world use this distribution, but Amazon is available only in selected countries.
To turn off the Amazon search, click on the Dash Home and search for privacy. Then turn the switch "Include online search results" to off.

This will turn off all online searches in the Dash.

Installing Japanese input on Ubuntu 12.10

In my last post I wrote about the terminal command that will enable Japanese input in Qt-4 applications, for example Anki, a flash card program for studying languages or basically anything else.
On localizing Japan, a step by step introduction on how to install the IBUS system is laid out, but when I followed it, I had the problem, that the IBUS icon did not show up in the toolbar, so I found a terminal command to fix that:

ibus-daemon -drx

Also, on Ubuntu 12.10, Ibus-qt4 should already be installed by default if you use the software centre to install Japanese input, but it did not work. I uninstalled it using

sudo apt-get remove --purge ibus-qt4

And reinstalled it using:

sudo apt-get install ibus-qt4

Now, Japanese input is working, but we'll see how it goes...

Anthy Japanese Input in Anki

Anthy is an IBUS method to input Japanese characters, write in hiragana and click F7 for conversion to Katakana. This works fine in the standard applications, like LibreOffice, or Firefox, but does not work in Qt applications, as is Anki.

Qt is a cross-platform application framework that is widely used for developing application software with a graphical user interface (GUI). (from wikipedia)

To fix this I stumbled upon this solution:

$ sudo apt-get install ibus-qt4

Restart Anki, and it works.

Image processing using Fiji ImageJ and Adobe Photoshop / Illustrator

This is my workflow for processing SEM or TEM images to make them publication ready. Images from SEM are usually saved as tif files and come in two versions. One contains the scale bar and other information, the other one does not. I want to get the scale bar from one image and put it into the empty one: In Fij, I open both images and use set scale to extract the scale from the first image. I then set the same scale in the second image, and input a scale bar using Analyze -> Tools -> Scale bar.
Then I open the image in photoshop and crop it to size (8.25cm width, 600dpi) and turn it into grayscale.
Then I open the image in Illustrator and insert a scale bar (2mm high), with writing at 10pt, bold and Myriad Pro.

Installing additional LaTeX fonts using the command line

After installing LaTeX, I tried to compile a paper written using the achemso class. This is a class written and maintained by Joseph Wright for the journals of the American Chemical Society. Unfortunately, I did get some error, that related to a missing font. In the original achemso.dtx file it said that we need a few packages, one of them is mathpazo. This was not installed on my system so I downloaded an additional font package: sudo apt-get install texlive-fonts-recommended texlive-fonts-extra

Installing Driver for Ethernet Atheros Commuications AR8162

After I installed ubuntu I noticed a few major problems. The first is that I do not have any internet connection, neither ethernet nor wifi. So I needed to find out how to fix that.
First, I found out what controllers are installed using the lspci command.
The output (last two lines) gave me the following:
Network controller: Intel Corporation Centrino Wireless-N 2230 (rev c4)
Ethernet controller: Atheros Communications Inc. AR8162 Fast Ethernet (rev 10)

After googling around, I found out that the driver for the ethernet is not installed on my system, so I need to do that manually. As I did not have an internet connection, I downloaded the driver from this website. According to the forum post above, I need to use the following file:
compat-wireless-2012-02-28-p.tar.bz2

I saved it onto a flash drive and copied it onto the Desktop. Then I ran the following commands:

cd ~/Desktop
tar -xvf compat-wireless-2012-02-28-p.tar.bz2
cd compat-wireless-2012-02-28-p
scripts/driver-select alx
make
sudo make install

I got a lot of output, some referencing to the grub bootloader and Windows 7, so I rebooted into Windows 7 to check everything was still ok, which it was. I then booted back into ubuntu, and voila, the ethernet connection was working.

I then ran an update of Ubuntu using

sudo apt-get update