Debian Gnu Linux Packaging

2014 10 08

  • I am currently trying to package the Hekate software project. Andrew Holding kindly accepted to license his software under the GPL-3 license when I told him that the license he was using was not a Free Software license. Indeed, while the Creative Commons Attribution 4.0 International Public License is fine for licensing his Open Access-like scientific article, it might not qualify as a Free Software license because it does not explicitly allow modification of the work and redistribution of the modified work. Andrew was quick at dual-licensing his software with the GPL-3 license so as to allow the packaging of Hekate for Debian GNU/Linux. Read his paper at the ACS or at the NCBI Pubmed Central.

2014 august

  • I finally take some time to write about it: libwildmagic is now fully packaged for Debian. This has taken a long while because I worked with the upstream author to build true GNU/UNIX shared object libraries, with full qualifiers, like the SONAME and NEEDED fields in the libraries. The whole experience amounted to writing raw Makefiles! The OpenMS mass spectrometry library that I also package for Debian will make use of the libwildmagic libraries soon. This actually was the reason why I started packaging libwildmagic libraries for Debian in the first place.

2013 09 01

  • Finally Proteowizard is now in Debian ! Again, kudos to Brian Pratt for solving the licensing issues and make the documentation easily usable for packaging. He has been very friendly during our numerous mail exchanges. Let's start testing the library. It's not that packaging such a large software project is the last step, it is in fact the first step in doing real work with it!

2013 02 14

I now have almost terminated the packaging of two mass spectrometry beasts: OpenMS / TOPP is in experimental and Proteowizard still requires some fixes for licenses... Other smaller projects are in testing right now:

  • OpenMS / TOPP (packaged as libopenms and topp). I must thank the following people with whom I had numerous emails exchanged: Oliver Kohlbacher, Stephan Aiche, Timo Sachsenberg;
  • Proteowizard (packaged as libpwiz). Many thanks to Brian Pratt ( for quick bug report response, for accepting modifications to the source package to fit my needs and also for his high availability and kindness.
  • pymzML (packaged as python-mzml). Thanks to Christian Fufezan for quick bug report response, for accepting modifications to the source package to fit my needs and also for his kindness;
  • X!Tandem is packaged as tandem-mass (Olivier Langella, who initially produced incomplete Ubuntu packages accepted my fixes and thus I could upload it to testing. I was sad to notice that this project is not responsive on questions and remarks. Maybe they have no time to bother? I acknowledge that they answered indirectly to a question of mine, by setting all the documentation available on their site on the same license as the software (Artistic license), which was not explicitly written before I wrote to them on that subject.

These packaging efforts are the first attempt to package as much mass spectrometry-related software as possible for Debian GNU/Linux. Mass spectrometry for biology is a scientific/technical discipline that has become widely popular only rather recently, when compared with older biology disciplines, like genetics or biochemistry. Thus, while biology has its ways deeply rooted in free/open software (think software to align DNA sequences...), mass spectrometry has lagged behind in the Free Software respect. It is only since some years that I feel that people doing mass spectrometry and writing software for mass spectrometry are acknowledging the power of Free Software and of the corresponding licenses. I think the mass spectrometry community is now mature enough on these questions to address the problems of making all the software produced under Free Software licenses available on a rock-solid platform as Debian GNU/Linux is.

In the Free Software world, we have all the tools required to develop software and elaborate powerful solutions:

  • C/C++ compiler
  • Python
  • Databases (Postgre/SQL, MySQL)
  • PHP
  • ...

Which makes me sad when I see people develop software using proprietary stuff like C#/DotNet and the likes. When the packages above have entered Debian main, I'll properly test them, let people know they are available and start contacting people to see if a global mass spectrometry community can form around Free Software for mass spectrometry.

Latest news 2011 06 05: I did my first massXpert upload as a Debian Developer (lopippo [!at!] debian [!dot!] org) !

One way to get involved in a GNU/Linux distribution is to package software for that distribution. Indeed, the competing distributions, like Fedora, Ubuntu, Mandriva... try to provide as much software as possible. Providing software well packaged by competent developers is not something trivial. Debian GNU/Linux is certainly the distribution that provides the greatest number of software packages of the highest quality.

My involvement in Debian started some years ago, with my great friend (and Debian Developer, DD) Lionel Mamane. He has served as a mentor and helped me package the first programs I wanted to get into Debian. Packaging for Debian is certainly not something easy and being mentored is almost unavoidable if one wants to progress at a detectable pace. When a package is ready, the mentor (who needs to be a DD) can upload the package to the Debian servers (this is called sponsoring a package).

Once the Debian packaging is well understood and when the packages are in a good shape, the packager might ask for upload rights, that is to be allowed to upload the packages himself without having to be sponsored by a Debian developer. In Debian, packagers who want to contribute to large software projects can team-up and create teams of packagers with well-defined goals. I participate in two groups of packagers : Debian science and Debian chemistry.

The packages I currently maintain in Debian are listed here.


Free Software


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