Hi- Nice list.
This project is a container for a set of useful (to our group) tools developed over the years. The intent was to release the more useful ones individually -- as was done for leaff/sim4db -- but the time and/or support was never quite there. The wiki page http://kmer.sourceforge.net/wiki/index.php?Main_Page lists the most useful tools. Unfortunately, there is also a lot of crap in there that shouldn't be installed. I can probably package up those tools -- ESTmapper, ATAC, and meryl -- without too much trouble. The meryl package will be the same bits that are included in wgs-assembler/kmer now. Looking at what is built now, there will still be some crap left over. wgs-assembler needs only the libraries and header files. I'll drop a line when this gets done. seagen/seatac are components of ESTmapper/ATAC (respectively) that aren't useful standalone. tapper and trie are two (of many) tools that failed to pan out. Unrelated to kmer, wgs-assembler also needs several of the PacBio codes ( https://github.com/PacificBiosciences) to run a specific use case. I don't have a list of what is required - I've never installed these personally. Perhaps https://github.com/PacificBiosciences/SMRT-Analysis will capture everything. That is, at least, their primary analysis suite, if not the latest bits. b On Sun, May 3, 2015 at 10:32 PM, Afif Elghraoui <[email protected]> wrote: > 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 > > -- > Afif Elghraoui | عفيف الغراوي > http://afif.ghraoui.name > > 1. https://wiki.debian.org/UpstreamGuide >
