Ubuntu Repository

by levien on di 29 april 2008 // Posted in misc // under


The original repository was getting a bit outdated. It was trailing a few Ubuntu-releases behind and only had i386-builds. You can still use it for Hardy or manually download packages (see below) for installation on newer releases, but I'm no longer going to maintain the old repository. Instead, most packages have been moved to my personal package archive (PPA) on launchpad.net. Please check there for instructions and the newest 32-bit and 64-bit builds for Ubuntu (and Debian) Linux...

Go to the new PPA

Quick installation of the main packages:

sudo add-apt-repository ppa:levien/thbio ; sudo apt-get update
sudo apt-get install cash grind sqiv xppaut


Below you will find the old zonnetjes.net Ubuntu repository. This repository contains a number of useful packages for older Ubuntu versions (8.04, 7.10 and 7.04). Most packages are related to theoretical biology, science in general and spatial (GIS/GPS) data processing. The general APT source for the old repository is:

deb http://levien.zonnetjes.net/ubuntu ubuntu extra
deb src http://levien.zonnetjes.net/ubuntu ubuntu extra

You can also download the Debian packages manually from http://levien.zonnetjes.net/ubuntu/pool/extra/


To add this repository to the packages available in your Ubuntu, Xubuntu or Kubuntu installation, follow these steps:

  • Make sure you have the Universe and Multiverse repositories enabled in your package manager, as many of our packages depend on this. You can select repositories from the configuration menu, under System->Administration->Software Sources. See the Ubuntu wiki for more detailed instructions.
  • Add this repository to your APT sources by executing one of the following commands from a terminal:
  • Add the GPG key for this repository:



  • 2009-11-14: Started moving packages to https://launchpad.net/\~levien/+archive/thbio Please test the new builds and let me know if they work!
  • 2008-05-06: Added thbio-binf package and updated thbio-main.

Known Issues / TODO

  • The grind_2.05-01 package is broken, as the main script refers to my build directory and therefore fails on other machines. Please use grind_2.05-02 instead!
  • The thbio-binf meta-package currently does not work with Feisty, some dependencies need to be fixed.
  • This repository currently only works with the 32-bit Intel version of Ubuntu. It would be nice to at least have a 64-bit version of all packages. However, I only have 32-bit hardware, so I could use some volunteers to help compile and test things on a 64-bit Ubuntu installation...
  • Add packages for libsfmt and libdsfmt (fast SSE2 implementations of the Mersenne Twister RNG)
  • Add texlive-extra-utils (which provides the rather useful tool epstopdf) as dependency to to thbio-main
  • Add a number of useful scripts to thbio-main
  • content: Fix compilation problems and makefile in the source package