On Thu, Jan 10, 2019 at 09:42:03PM -0500, Joshua Marshall wrote: > Does anyone on this list have an interest or use case for Hmmer2? I'd like > to put a pin in this.
I have no idea, I'm not using it but I'd love to help you. I've checked https://github.com/MichiganTech/hmmer/releases and https://github.com/anadon/hmmer2/releases Both are featuring version 2.5j (both dated 2018-11-01). I'd give the repository a try for packaging whatever is found there as tagged release that you specify as "the reference repository for hmmer2". Hope this helps Andreas. > On Fri, Jan 4, 2019 at 12:42 PM Joshua Marshall <[email protected]> wrote: > > > PVM is no longer maintained, and hasn't been for quite some time. The use > > case for when PVM is relevant is when RAM on individual machines was closer > > to 16M. Given that we have $5 computers with 256MB, I find it reasonable > > to tell such users to upgrade. > > > > As for interpro-scan, most of the documents got updated for the project > > and it is easier to set up locally. However, there is still a large amount > > of work that goes into updates every few days to a few weeks and users > > should rely on the service rather than a package. If you do want to have > > the package, you need a employee charged with it's regular updates and > > development because of how involved and federated that particular program > > set is. > > > > On Fri, Jan 4, 2019 at 10:41 AM Steffen Möller <[email protected]> > > wrote: > > > >> Hello Joshua, > >> > >> I would be much of a fan to see interpro-scan redistributed with Debian. > >> Andreas' concern is that nobody understands what happened. We have > >> Hammer2 in our distribution https://packages.debian.org/sid/hmmer2 and > >> if your work is plain compatible then I don't see why it should not > >> substitute it. Is there a way to keep hmmer2-pvm? There are not too > >> many on https://qa.debian.org/popcon.php?package=hmmer2 using it but I > >> would not want to ruin established services anywhere with an apt-get > >> update. > >> > >> Best, > >> > >> Steffen > >> > >> On 04.01.19 16:25, Joshua Marshall wrote: > >> > Hello all, > >> > > >> > In Spring 2018 I was working on packaging interpro-scan for some > >> > work. There were a number of packages which has some build or test > >> > failures which I worked on. Of these, Hmmer needed some more > >> > attention. Originally, this was an upstream request to tweak their > >> > autoconf but that went bizarrely bad. At that point, I went in to fix > >> > up a decade's worth of technical debt. Of these were removal of > >> > Parallel Virtual Machine support, adjusting buffer sizes upwards for > >> > memory found on modern systems, hard code enabling of pthreads, > >> > renaming executable to hmmer2 in the build to not conflict with hmmer > >> > or hmmer3 to allow for parallel installation, and simplification of > >> > the configuration header. All unit tests pass. There is a need for > >> > parallel installation of hmmer2 and hmmer3 because hmmer2 works on a > >> > global genome scale, while hmmer3 is build to only operate on parts of > >> > the genome. > >> > > >> > This should have do change in behavior or output in any way except for > >> > removal of PVM support and minor runtime changes. This change set > >> > should be viewed strictly as a technical debt clean up. > >> > > >> > On Fri, Jan 4, 2019 at 1:11 AM Andreas Tille <[email protected] > >> > <mailto:[email protected]>> wrote: > >> > > >> > Hi Joshua, > >> > > >> > On Thu, Jan 03, 2019 at 04:45:33PM -0500, Joshua Marshall wrote: > >> > > Is now a better time to bring up my Hmmer 2 fork? > >> > > >> > Please shortly describe the purpose of your fork the changes you > >> > did on the list and than we can (probably/hopefully) replace the > >> > existing hmmer2 package by your fork. I'm *not* a hmmer2 user > >> > (nor do I have the slightest idea what hmmer2 is doing - I'm not > >> > a biologist) so it makes no sense to discuss this just with me. > >> > Thus I'm posting this on the list. > >> > > >> > For other readers here are some links to previous posts about > >> > this issue: > >> > > >> > > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066203.html > >> > > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066757.html > >> > > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066762.html > >> > > >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-November/066997.html > >> > > >> > My prefered way to deal with this would be to point the debian/watch > >> > file of hmmer2 to > >> > > >> > https://github.com/anadon/hmmer2/releases > >> > > >> > and package the latest release from there (instead of applying huge > >> > patches that nobody can read or maintain) but please document the > >> > relation to the official hmmer2, your fork/continuation and hmmer3 > >> > at an easily accessible place. > >> > > >> > Kind regards > >> > > >> > Andreas. > >> > > >> > > On Sun, Oct 28, 2018 at 4:47 PM jrmarsha <[email protected] > >> > <mailto:[email protected]>> wrote: > >> > > > >> > > > I'm sorry. > >> > > > > >> > > > On 10/28/18 4:15 PM, Andreas Tille wrote: > >> > > > > Hi, > >> > > > > > >> > > > > the list is archived: > >> > > > > > >> > > > > https://lists.debian.org/debian-med/2018/10/threads.html > >> > > > > > >> > > > > Please do not expect always prompt responses - sometimes > >> > volunteers > >> > > > > have other things to do. > >> > > > > > >> > > > > Kind regards > >> > > > > > >> > > > > Andreas. > >> > > > > > >> > > > > On Sun, Oct 28, 2018 at 09:03:27AM -0400, jrmarsha wrote: > >> > > > >> Hello, > >> > > > >> > >> > > > >> > >> > > > >> I've tried sending a few messages but I've gotten no > >> > response. Are they > >> > > > >> making it to the debian-med mailing list. > >> > > > >> > >> > > > >> > >> > > > > >> > > >> > -- > >> > http://fam-tille.de > >> > > >> > > -- http://fam-tille.de
