[Debian-med-packaging] Debian package for vsearch

[Torbjørn Rognes]

Hi Andreas

On 18 Feb 2015, at 16:18, Andreas Tille <andreas at an3as.eu<mailto:andreas at an3as.eu>> wrote:

Hi Torbjørn,

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.


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.

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

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.


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.

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.



Kind regards and thanks again for the very important free tool

     Andreas.

--
http://fam-tille.de

Best wishes,
Torbjørn Rognes
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