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Re: Hmmer2 fork / enhancements (Was: Is my post making it to the mailing list?)

I've thought I've answered questions a few times.  Are messages getting dropped?  I didn't get the one just before from Steffen. 

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PVM is no longer maintained, and hasn't been for quite some time.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
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