Does anyone on this list have an interest or use case for Hmmer2? I'd like to put a pin in this.
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 PVM is no longer maintained, and hasn't been for quite some time.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 >> > >> >
