Hi, Afif- I (finally) added downloads for meryl and some others. They're linked from the kmer homepage http://kmer.sourceforge.net/
Documentation remains weak, and might improve in the next few months as we close out a few projects. You only need the meryl package: http://sourceforge.net/projects/kmer/files/meryl-r2008.tar.bz2/download b On Wed, May 20, 2015 at 2:03 AM, Afif Elghraoui <a...@ghraoui.name> wrote: > Thanks for your reply. Please see inline: > > On الثلاثاء 19 أيار 2015 07:15, Brian Walenz wrote: > >> I'm a little slow on packaging up a release, sorry. It's on the to do >> list with a decent priority, but not getting much time yet. The paying >> projects are being unruly. >> >> > No problem. > > From the kmer repo, I've created four releases by removing select top >> level directories. For 'meryl' the directories are: >> >> Make.include >> Make.rules >> Makefile >> README.compiling >> README.meryl >> configure.sh >> libbio >> libkmer >> libmeryl >> libseq >> libutil >> meryl >> >> > Thanks; this is very helpful. README.meryl is not on sourceforge, though. > At least not that I saw. > > > No changes to Make* are needed. This is the package needed for >> wgs-assembler. The other three are for ATAC, ESTmapper and sim4db >> (which exists already). >> >> I've wanted to get rid of kazlib for a long time, and I think it is only >> used by the atac package. Before you expend too much effort on >> modifications, lets see if the meryl component will compile without it. >> > > I can verify that it does. > > IIRC, it's used only in class 'bigQueue' in libutil. I wanted to >> replace it with STL, but last time I looked, it wasn't a drop-in >> replacement. >> >> The test suite(s) are probably quite low level, and not very good. A >> functional test should find any major problems. I can't think of any >> gotchas for reviving the tests though. >> >> > Ok, so I guess I'm all clear for tackling that. > > I'd like to lay out the full status, even though some of these items are > not for the short-term. The short-term package looks like it will just > provide meryl so that we can climb the dependency chain to wgs-assembler > and other packages that use it. The rest of the code requires a little > clean-up as I understood from you. > > * Short-term plan for first version of the package -- meryl only > I can put this through on my own without additional action from your side > (but the README.meryl file would be nice to have). I would work on the > following: > - build shared libraries rather than (or in addition to) static, as > preferred for official Debian packages [1]. If you think this isn't a good > idea, there is potentially some flexibility here. > - create man pages for executables > > * longer-term plan -- remaining components + general improvements > This part can wait until you complete the clean-up you mentioned in your > first message. The steps here for me are: > - include the remaining components and, same as for meryl, make shared > libraries and man pages > - You have a copy of mt19937ar in your distribution, which as of now is > not packaged in Debian. I haven't checked to see if you patched this code > or if it's an unmodified copy. At some point, mt19937ar would need to be a > in a separate Debian package that kmer would just depend on. > - fix test suite. I will also see how well this goes for meryl. If it > doesn't take too long, I can have it be part of the package-build process. > > > Thanks and regards > Afif > > 1. https://www.debian.org/doc/debian-policy/ch-sharedlibs.html > > -- > Afif Elghraoui | عفيف الغراوي > http://afif.ghraoui.name >
