How to build MySQL Workbench on Ubuntu Precise (pre-release)

Update 2012-04-25: mysql workbench has now appeared in the universe package archive. You should be able to install it with a simple:

sudo apt-get install mysql-workbench

Read on if you still want to compile from source.

Right now (2012-04-04), Ubuntu 12.04 hasn’t been released yet, and so there is no binary package from Oracle of MySQL Workbench for Precise. I managed to get the MySQL Workbench binaries for Oneiric to run, by manually installing libzip1_0.9.3-1_amd64.deb from Oneiric, but this wasn’t stable (crashed as soon as I tried to run a SQL Query).

So I decided to build from source. Here’s how I did it

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SQuirreL SQL: a nice database GUI frontend for Ubuntu

Here at MalariaGEN, we use MySQL extensively, and there are myriad nice GUI tools for accessing it from our Ubuntu desktops. However, we also use Microsoft SQL Server for some of our particularly large laboratory data, and we wanted to access MS SQL Server databases on Ubuntu (11.04 Natty Narwhal) with a GUI, preferably with open source software.

Here is how to set up one such tool (SQuirrel SQL). Note that we will install the application system wide; it is also possible to install it in your home directory, and to create the custom launcher in .local/share/applications if you like. We’re focussed on the install process on Ubuntu 11.04 with Unity, but these instructions should work on other modern linux distros without too much modification.

Ubuntu Cloud Days

As we’re starting to get into cloud technology in a big way here, I decided to take part in Ubuntu’s IRC training days on the subject, Ubuntu Cloud Days.  While the material covered was often more low-level than what we are likely to use in the short term, I found the sessions on Ensemble and CloudInit to be particularly useful, as they’ll be directly applicable to our upcoming GWAS work on the ec2 cloud.

Ubuntu on Amazon EC2 from scratch

Update: I’ve now rolled this blog post into the Ubuntu wiki’s: EC2 Starters Guide page. Hopefully this helps out the Ubuntu community!

The informatics team here at MalariaGEN have been working with ec2 since before I joined them. So naturally, it’s one technology with which I’ve had to come to grips in the course of doing my job. For me, EC2 had a fairly steep learning curve, and after spending a while trying to learn it through doing, I decided that I would just have to spend some time getting properly to grips with how things worked. As part of that I decided to document it in a way that I’d not yet seen on the web: logically, comprehensively, explaining all the strange concepts and quirks that were clouding my understanding and stopping me from getting my job done efficiently.

Ubuntu’s Ambiance: selected items in unfocused windows are invisible

I have a confession to make: I really like Ubuntu’s design, its look and feel, and its colour scheme. And it seems to get better with each release. The new Natty theme is really beautiful, and the dark window decorations of the Ambiance theme are great (especially now that they’ve chased down the odd dark text on dark background problems).

Having said that, there’s one thing that I really don’t like: the way that it’s virtually impossible to tell what you have selected in windows other than the one that happens to be focused. This is because the focused elements get completely desaturated, like this:

Which items are selected? It's anyone's guess!

Gridengine the Ubuntu/Debian way

I’ve had Sun GridEngine running on our cluster of 12-core HP blades from its earliest days. What has not been working is the the inter-host communication (the ability of the system to schedule and distribute jobs across the nodes). I therefore set out to fix this situation. It turns out that the problems that prevented this from working are mainly caused by quirks in the way that the Debian (and by inheritance, Ubuntu) packaging was done.

Ubuntu on EC2

This is just a short post to say, if you’re into Ubuntu, and you’re into Amazon EC2, then Eric Hammond’s alestic.com, Scott Moser’s blog, and the ec2-ubuntu mailing list are indispensable resources.