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Debian packaging of phylophlan and using vsearch instead of usearch

Hi Nicola,

I'm writing to you on behalf of the Debian Med team which is a group
inside Debian that intends to package Free Software in the field of
biology and medicine for main Debian.  I received a user request to
package phylophlan and have created some packaging code[1].

The packaging involved some tweaking since the code belongs to
/usr/share/phylophlan since it is not changable while the data need to
be unpackaged (and thus written by users) and so were moved to
/var/lib/phylophlan.  This patch[1] is not a big deal and could remain
for the Debian packaging exclusively.

However, there is a problem with usearch.  We can not package this tool
for Debian since it is non-free and we are not allowed to build it from
source.  The good news is that there is a free replacement vsearch[3].
So I tried to create a patch to use vsearch instead of usearch[4].  When
doing so I learned that both tools are not compatible regarding command
line options and phylophlan might need some better adaption than the
very simple patch[4] I used.

Before I'd dive more into the details I'd like to know whether you would
be interested in supporting vsearch in parallel to usearch in phylophlan
or whether you leave us on our own with developing and maintaining the

Kind regards and thanks for providing phylophlan as free software


[1] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylophlan/trunk/
[2] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylophlan/trunk/debian/patches/datadir.patch?revision=22007&view=markup
[3] https://github.com/torognes/vsearch/
[4] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch?view=markup


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