On Sun, Jan 13, 2019 at 09:22:13PM -0500, jrmarsha wrote: > I've thought I've answered questions a few times. Are messages getting > dropped? I didn't get the one just before from Steffen.
I did not received any answer to https://lists.debian.org/debian-med/2019/01/msg00046.html and the web archive has no answer as well. > On 1/13/19 3:57 PM, Andreas Tille wrote: > > [Re-add mailing-list] > > > > Since we should offer it I did the packaging but there were some > > questions about details remaining. > > > > Kind regards, > > > > Andreas. > > > > On Sun, Jan 13, 2019 at 09:50:18PM +0100, Steffen Möller wrote: > > > We should still offer Hmmer2 in our archive since > > > > > > a) it is a piece of history > > > > > > b) rounds up functionality from other libraries in Perl/Python > > > > > > c) Homebrew and Conda also feature it. > > > > > > d) > > > https://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0163-0 > > > > > > Cheers, > > > > > > Steffen > > > > > > On 11.01.19 09:42, Andreas Tille wrote: > > > > 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 PVM is no longer maintained, and hasn't been for quite some time.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
