Tag Archives: ubuntu

Build & Install Osra 1.3.8 on Ubuntu 11.10


Osra is a a utility designed to convert graphical representations of chemical structures create by Igor Filippov at the National Cancer Institute. This page documents how to compile and install Osra on Ubuntu Linux 11.10. These instructions may work on other versions of Ubuntu Linux and on Debian Linux.  Please leave a comment if you have compiled Osra using these instructions on a different version of Ubuntu, or on other Linux distributions.


At the time of writing this doc, March 2012, the Osra version is 1.3.8 and is available at:

I copied all the source to a directory in /tmp. If you need the source code at some later point in time, don’t use /tmp as files in /tmp are deleted upon reboot (if they’re older than 14 days). Also, at the time of writing Osra requires a patched version of Gocr for Osra to work. You need to install Gocr before you try to compile and install Osra, you also need to install other packages required for Osra to compile. Most are listed below, but see the Osra Homepage for more details.

An overview of the steps are:

  1. Install required Ubuntu packages
  2. Compile and Install Gocr
  3. Compile and Install Osra

I’ve also written instructions on how to install Osra 1.2.1 on Ubuntu 9.04, however that was written in 2009. Continue reading Build & Install Osra 1.3.8 on Ubuntu 11.10

Ubuntu Jaunty & ATI

This is quick’n’dirty writeup to help others who might have the same problem. I’ll clean this up later in the week …

Ubuntu Jaunty is the new beta version of Ubuntu. It comes with a new version of X.Org and the ATI drivers have been incompatible with this version of X.Org. ATI recently released drivers that support X.Org 1.6. If you have problems with X not starting follow the instructions here:

For me what happened is that X wouldn’t start properly and cause my Lenovo T400 to freeze and lock up. The laptop would boot but when X would start (when the login screen appears) I’d get a black screen with red lines at the top. To solve this I booted to runlevel 1, also known as failsafe mode. If your using a laptop with wireless, I suggest you connect directly to your router using a network cable, otherwise you may have to configure wireless manually (it’s not that hard).

When your system starts, select failsafe mode, on the next screen to appear choose the option to go to a “root shell with networking”.

Next remove the install ATI drivers and install from scratch the ones you need:

sudo apt-get remove –purge xorg-driver-fglrx xserver-xorg-video-ati xserver-xorg-video-radeon
sudo apt-get install xserver-xorg-video-ati
sudo apt-get install –reinstall libgl1-mesa-glx libgl1-mesa-dri
dpkg-reconfigure -phigh xserver-xorg

If this doens’t work for you see the Ubuntu page mentioned above.

Xen for Ubuntu Intrepid 8.10

I was in the process of figuring out and documenting the process of  compiling and installing an Xen enabled kernel on Ubuntu Intrepid 8.10. This was for a specific project that’s not going to come to fruition. I’m not going to bother as I also don’t feel like having my laptop burn a gaping hole through my lap as I wait for the kernel to compile, and well you know I still have some use for the 2 lads downstairs. And after years of compiling kernels, I really can think of more productive uses of my time.

The quickest way is to grab a Debian Xen enabled kernel, this isn’t recommended by Ubuntu and if your not comfortable hacking your system and having to compile modules (drivers in Windows speak) for hardware or proprietary hardware that Debian doesn’t include support for, then don’t even think of doing this and just use KVM.

Here’s how Chris did it for a system running a AMD64 processor, if you’ve an Intel processor you’ll need to use a different kernel:


If you want a later kernel (2.6.27 or 2.6.28) poke around:


That’s the approach I’m going to use, as I know that if I’ve problems or issues I’ll be able to figure it out. Anyways, the start of the orignal draft is below, preceded by a minor rant. When I get around to getting Xen on Ubuntu to work with a Debian kernel I’ll add a new post here. Continue reading Xen for Ubuntu Intrepid 8.10

WordPress 2.7.1 Editor

I recently upgraded this WordPress installation from 2.7 to 2.7.1 using Dreamhost’s upgrade tools. However, the friggin’ feckin’ post editor is busted, at least in Firefox 3.0.6 on Ubuntu Intrepid. I can still use the QuickPress editor, which is only good for basic posts. If I want to add images or files, I’d have to manually upload them and link to them … anyways what a pain. If your planning on upgrading to WordPress 2.7.1 I’d suggest you wait a wee bit.

The problem I’m having is that on the “New Post” page, where the categories sections should be is instead an embedded (maybe an iFrame) of the WordPress Dashboard. When I try and type in the editor the pages changes to a near blank page with only the editor buttons showing. Grrrr …

I’ve tried the following steps (recommended on various sites and forums) to no avail:

  • Disabled all plugins
  • Disabled Google Gears
  • Cleared the browser cache

However, it works fine in KDE’s Konqueror browser. When I get the time, I may compare the generated HTML, and see if I can determine what’s causing the problem. Here’s a screenshot … sheesh now I can’t even insert a screenshot using Konqueror gotta do it manually. Look at the “Categories” section on the right-hand side:

Enable mod_perl on Debian, Ubuntu, & Other Linuxes.

To enable mod_perl with Apache2 on Debian & Ubuntu for all directories served up by Apache2, including user directories such as ~/public_html, add the following lines to /etc/apache2/sites-available/default

# enable mod_perl
    <Files ~ ".(pl|cgi)$">
           SetHandler perl-script
           PerlResponseHandler ModPerl::Registry
           Options +ExecCGI
           PerlSendHeader On

In a real production environment you probably don’t want to enable this for all directories that Apache2 serves up, but only from those directories you expect to run perl in.

Thanks to this thread on the Ubuntu Forums for the info.

Titled updated as per Ozkar’s suggestion.

Dell Laptops & Ubuntu

I’d heard that Dell were offering Ubuntu Linux on some of their laptops and I hadn’t really looked into it. But I came across this page the other day and it’s pretty neat to get Ubuntu (or any Linux) preloaded on a laptop from a major vendor:


It’s good to support coming from a major vendor, and Dell even offer’s a repo so you can get BIOS updates for support hardware:


However, I’m still partial to getting Lenovo’s T400 over a Dell.

Lenovo Laptop?

I’m thinking of getting a new laptop either the Lenova ThinkPad T400 (which is a replacement for the T61), or the IdeaPad U330 to replace my aging Dell 700m

The big thing for me is do they work with Linux (for me specifically Debian or Ubuntu).

For anyone interested in either laptop, looks like the the U330 works (near) flawlessly with Ubuntu. See this posting on this thread for an enthusiastic comment:


And with the T400 you’ll have some work to get everything working smoothy. Such as the dual-graphics cards which is how Lenovo get’s up to 10 hours of battery life from the T400.

However, if you don’t mind using breaking stuff, the new Beta version of Ubuntu appears to work reasonably well on the T400. See this blog posting and this thead on Lenova’s forums for more details.

I’m torn between either, the small size of the U330, versus the better battery life of the T400 (and the fact that both are a weeeeee bit dear).

OK, I’m tired as I write this, and I find sometimes when I “blog while tired” that my grammar/spelling/ability to make sense suffers, so maybe I’ll rewrite this in the morning. 🙂

e17 on Ubuntu Revisited

Ever since my original post on installing Enlightenment E17 on Debian and Ubuntu things have changed, such as the server that hosted the package repositories for both Debian & Ubuntu going off-line (supposedly temporarily but it’s been offline for almost 6 months).

Also, I’ve been having issues with E17 working correctly on my laptop running Ubuntu. This is probably because of conflicts between old and new packages, and because E17 is still beta code.

In this posting I’ll concentrate on installing or reinstalling E17 on Ubuntu 8.04 otherwise know as Hardy Heron. You should be able to use the same instructions to install E17 on other recent versions of Ubuntu. I’ll also try and the same for installing E17 on Debian at some point in the future.

First, remove all existing traces of any previous E17 installs.

sudo apt-get remove --purge e17 emodule* libevas* libefreet*

You’ll notice that I’ll use a mixture of apt-get and aptitude to remove and install packages. I’ve found that sometimes aptitude is a little too aggressive in removing packages, and sometime will remove package that I need. For instance when I started to remove E17, aptitude also wanted to remove xserver-xorg which would mean X wouldn’t work (no GUI).

Next, remove any old repositories for E17 from you sources.list. But, first make a back-up copy of the file:

sudo cp /etc/apt/sources.list /etc/apt/sources.list.bak

Then, remove or comment out any other E17 repositories from the file, by editing the file with your favourite text editor. I normally use emacs:

sudo emacs /etc/apt/sources.list

Or if you don’t have X running and are doing this from a console:

sudo emacs -nw /etc/apt/sources.list

You can use # to comment out lines. Remove any references to edevelop.org or soulmachine.net .

Then, add the dunnewinde.net repository, by adding the following lines:

# dunnewind e17 repository for Ubuntu Hardy
deb http://e17.dunnewind.net/ubuntu hardy e17

You can replace hardy with either gutsy or feisty if your running either of those versions of Ubuntu.

Now your ready to install/reinstall Enlightenment E17! 🙂

sudo aptitude install e17

Or if you also want to play with a media player based on E17 libraries install eclair also.

sudo aptitude install e17 eclair

Once the install is completed, logout. At the login screen (GDM) change your session to Enlightenment and login and you should see something that looks like the following:

Sorry that screenshot is missing. I deleted it as someone was leeching the image by linking directly to the image from their blog (using up my bandwidth instead of theirs). I’ll upload a new image in the near future.

No other themes are installed, I’ll write another post in the next few days showing how to get themes from get-e.org and install them. In the meantime here’s a screen-shot using the Darkness theme:

This posting originally at: