June 2008

Eclipse 3.4 (Ganymede) on Ubuntu

These instructions refer to outdated version of Eclipse and Ubuntu. Please refer to the new instructions on installing Eclipse Galileo (3.5) on Ubuntu Jaunty (9.04)

Eclipse Ganymede (the successor to Europa) was released today. Ubuntu seems to be stuck on Eclipse 3.2 since at least Feisty Fawn. There are nice features that we are missing out on (Mylyn, inline renames, etc.). JDK First things first, you need a JDK (Java SDK) in order to use Eclipse. I am a fan of the OpenJDK, Sun's open source version of its JDK. OpenJDK recently reached full Sun JDK compliance. But any JDK should work, assuming it is at least Java 5.

sudo apt-get install openjdk-6-jdk

Then update your ~./bashrc file, appending the JAVA_HOME (adjust this if you use a different JDK).

export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/

Get Ganymede

wget http://ftp.osuosl.org/pub/eclipse/technology/epp/downloads/release/ganymede/R/eclipse-java-ganymede-linux-gtk.tar.gz
tar xzvf eclipse-java-ganymede-linux-gtk.tar.gz
mv eclipse eclipse3.4

We should be ready to go:


And your nice new Eclipse is up and running. Suggested Plugins Eclipse is great because it has so many plugins. I even use it as my default Python editor. If you go to Help > Software Updates, you will see a vastly improved update dialog (the previous one was painful). Here are my favorites:

Let me know what you think of the new Eclipse and if there are other plugins you just can not live without.

Update: As Scott points out in the comments, there is an open request on launchpad to include a more recent version of Eclipse in the Ubuntu repositories: https://bugs.edge.launchpad.net/ubuntu/+source/eclipse/+bug/123064

pymedia on Ubuntu Hardy Heron

Recently, I needed to use pymedia, for some audio and video encoding. The problem though, is that pymedia was nowhere to be found in the Ubuntu Hardy Heron package repository, and the only .deb installation candidate from the pymedia website was for an older version of pymedia and Python 2.4. Not wanting to run an old version and having Python 2.5 as a requirement, I needed to compile the package myself--no easy task, it turns out.

Step 1: Get pymedia

wget http://internap.dl.sourceforge.net/sourceforge/pymedia/pymedia-
tar xzvf pymedia-
cd pymedia-*

Step 2: Get the pymedia dependencies

As noted here.

sudo apt-get install python-dev libogg-dev libvorbis-dev liblame-dev libfaad-dev libasound2-dev python-pygame

Step 3: Get GCC 3.4

Note pymedia will not compile with GCC 4.0.

sudo apt-get install gcc-3.4 g++-3.4
export CC=gcc-3.4

Step 4: Build/compile pymedia

python setup.py build

Step 5: Be a good Ubuntu user with checkinstall

Checkinstall is great because it installs the package as a .deb file.

sudo apt-get install checkinstall
sudo checkinstall python setup.py install

Note: If you want to be a bad Ubuntu user, you can run "sudo python setup.py install" instead of the checkinstall command.

Step 6: Try it out

>>> import pymedia

bminews.com launched

I am launching a social news site, bminews.com. It is a specialty site for practitioners in the fields of Bioinformatics and Medical Informatics. Join in! I am looking for a site with great news on new developments, technologies, and opportunities in the field. Related topics (programming/consulting/career advice/math/scientific writing/conferences) are all encouraged.


I have been working on an open source project, jsonpickle. The goal of the project is to be able to serialize a Python object into standard JSON notation. Python can "pickle" objects into a special binary format, but sometimes it is nice to get a human-readable format. Especially with projects like CouchDB that have use a JSON-based API. jsonpickle is on its seconds release and can now officially handle Mark Pilgrim's Universal Feed Parser. Feel free to join in by finding bugs and working on the code! It is pretty easy to use:

>>> import feedparser, jsonpickle
>>> doc = feedparser.parse("http://feedparser.org/docs/examples/atom10.xml")
>>> pickled = jsonpickle.dumps(doc)
>>> unpickled = jsonpickle.loads(pickled)
>>> doc['feed']['title'] == unpickled['feed']['title']