Re: Hmmer2 fork / enhancements (Was: Is my post making it to the mailing list?)
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 <jrmarsha@mtu.edu> 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 PVM is no longer maintained, and hasn't been for quite some time.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 <steffen_moeller@gmx.de>
> > > > > > 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 <andreas@fam-tille.de
> > > > > > > > <mailto:andreas@fam-tille.de>> 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 <jrmarsha@mtu.edu
> > > > > > > > <mailto:jrmarsha@mtu.edu>> 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
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