[Debian-med-packaging] Debian package for vsearch

Andreas Tille andreas at an3as.eu
Wed Feb 18 22:29:36 UTC 2015

Hi Torbjørn,

thanks for your prompt reply.

On Wed, Feb 18, 2015 at 04:38:05PM +0000, Torbjørn Rognes wrote:
> > I'd like to inform you that the Debian Med team has created an official
> > package of vsearch for Debian.  We are really excited about your work
> > since this enables us to create fully functional free qiime packages as
> > well.  Thanks for releasing vsearch as free software.
> Thank you for creating a Debian package for vsearch! We very much appreciate your effort and hope this will make it easier for users to start using vsearch.

You are welcome.  We try to package anything that might be useful for
biology and medicine.  If it happens that you consider some other tool
developed or used by you or your group please let us know.
> > Since we uploaded the first package we received some bug reports about
> > compilation issues of vsearch.  These problems were addressed in patches
> > which are published in our packaging SVN at
> > 
> >   http://anonscm.debian.org/viewvc/debian-med/trunk/packages/vsearch/trunk/debian/patches/
> > 
> > It could be helpful if you would consider integrating the patches in
> > your next version since it could enhance the portability of vsearch.
> > 
> > Each patch has an header which also points to the according bug report
> > that is describing the problem which is resolved by the patch.
> > 
> > Please let us know what you think about the patches itself and whether
> > you are willing to include these.
> Thank you. We will consider all patches and potentially integrate all of them into a future version of vsearch. As far as I can see now they all seem to be fine. I will inform you when they have been integrated.

Thanks, that would be very helpful.

> There will probably be new versions of vsearch released with high frequency in the weeks ahead with bug fixes and minor improvements.

I just realised that new versions were released with a high frequency
and we try to catch up as good as possible.  Keeping us in touch will
definitely help to ensure that every version you regard as important
will be delivered as a Debian package.

> In line with what you have indicated in some of the packaging documents, we also plan to reorganize the file structure somewhat, perhaps removing some of the large data files and (old) executables, to make the size of the download smaller. We are also considering making just a single Makefile and integrating the code from zlib and bzip2 into our source tree. This will allow support for compressed input files and avoid additional dependencies.

Ahh, that sounds very sensible.
> I looked briefly on the website you provided a link to. There appears to be a misunderstaning regarding the author of the documentation. The following files seems to indicate that Robert Edgar is the author of the vsearch documentation (README.md, vsearch.1 and vsearch_manual.pdf):
> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/vsearch/trunk/debian/vsearch.doc-base.manual?view=markup
> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/vsearch/trunk/debian/vsearch.doc-base.readme?view=markup
> That is not the case. The documentation is written mostly by Frédéric Mahé, with some assistance from me.

Thanks for proof-reading which is very welcome.  I fixed this in SVN.
(Not sure whether "assistance from me" should be turned into a second
author or whether we should leave Frédéric Mahé.  You might like to know
that the doc-base registry in Debian is not widely used by Debian users
and thus the importance of this document is not very high.
> Robert Edgar is the author of the USEARCH software (http://www.drive5.com/usearch/), which is a closed source project. Only 32-bit executables are available free of charge for academics. VSEARCH is aimed as a free of charge, open source alternative to USEARCH.

Thanks for the clarification.
Kind regards



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