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Re: Debian packaging of phylophlan and using vsearch instead of usearch

Hi Nicola,

On Wed, May 25, 2016 at 07:56:08AM +0000, Nicola Segata wrote:
> Hi Adreas,
>   we recently updated PhyloPhlAn to support other usearch versions. I'm
> CC'ing Francesco (the lead on the project) which can be more accurate on
> which usearch version we need for the last version of PhyloPhlAn.

It would be nice to get some confirmation about the usearch version.
> Regarding other software I think it would be fantastic to have MetaPhlAn2
> as a Debian package. It's here: https://bitbucket.org/biobakery/metaphlan2 .
> It is widely used and stable (although we are further and actively
> developing it) and published a couple of times in Nat Methods.

I had a look into this.  It contains quite large binary data chunks.
Before I can seriously attempt to package this I would need to know
where and how theses data are obtained from, how to possibly change the
data (if this makes sense at all - if not why not) and what the
copyright of the data would be.  Otherwise Debian ftpmaster will refuse
the package to be uploaded.

> Another software we developed that would be great to have as a Debian
> package is GraPhlAn (https://bitbucket.org/nsegata/graphlan/wiki/Home)
> (Described here https://peerj.com/articles/1029/). It's a package to
> produce nice graphical representation of phylogenetic trees.

That's a really nice one. :-)  I injected packaging code into our
packaging version control system.  However, when doing so I noticed that
I need to package pyphlan[1] first.  I committed the needed packaging
code into our packaging Git and can confirm that the packaging of
graphlan works together with this precondition.  Before I can upload
pyphlan to the Debian mirror it would be great to have at least a
minimum three lines description, what the package is actually doing.  I
found something in the code that there are functions you would like to
see in Biopython (did you contacted Biopython authors about this - I
learned they are very responsive and open for enhancements) but I have
no real clue what the code is doing - except that its a precondition for 
graphlan.  So please provide some sensible description.

Another nice thing would to add a version tag to bitbucket.  This would
enable me to find a proper Debian package version which is currently
simply the date of the youngest file inside the download archive.

> Importantly, these two packages don't use any proprietary software so it
> should be easier to package them than PhyloPhlAn.

You are right but as I said above the binary data need some explanation.
> Let us know if you have any question and if we can help you somehow!

Thanks a lot for your nice hints.  We like to have this kind of
cooperation with upstream software authors.

Kind regards


[1] https://bitbucket.org/nsegata/pyphlan
[2] https://anonscm.debian.org/cgit/debian-med/python-pyphlan.git


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