Hello,
I'm contacting you on behalf of the Debian Med team. We are a group within the Debian project that focuses on packaging software for medicine and biology, making them easier to install and work with for users of Debian and its derivatives. Here is a list of biology software that we have packaged so far: <http://blends.debian.org/med/tasks/bio>
By way of trying to bring the Celera assembler into Debian, I have taken up packaging your project Kmer. I just have some questions/requests for you about issues that have come up.
Firstly, the licensing terms are not explicit in the source distribution for all components of your project. I only see license terms described for LEAFF sim4db. Although the sourceforge download page says GPLv2, We would feel more comfortable with an indication of this in the source distribution itself.
I also see that you offer the code only as subversion snapshots. Our packaging system works best with compressed tar archives (tar.{gz,bz2,lzma,xz}) and versioned releases. We would also like to avoid packaging a snapshot in the middle of partial development. What I have been working with so far is the snapshot matching that which was bundled with the latest version of wgs-assembler.
Finally, although not all components of kmer are used in wgs-assembler, I thought it would be good to include them all. I noticed, however, that there are some directories in your distribution that are not explained. I do not know the roles of some of these subcomponents. These are seagen, seatac, tapper, and trie. If you could please explain these, that would help me with creating their manpages.
The Debian project has a guide for upstream developers [1] that explains further some of these issues, but I have explained my main issues in this message. I'm sorry about its being a bit long.
Many thanks and regards,
Afif
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Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
1. https://wiki.debian.org/UpstreamGuide