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

Hi Andreas,

the usearch version for PhyloPhlAn is "usearch5.2.32". The newest versions of usearch are supported in a new version of PhyloPhlAn that is currently under development, so we cannot refer to this as stable.

About the errors you got from the "guide" example, did you run all the steps in order? Because if you only run "step3.sh", there would be missing files if the previous steps have not been executed.

About the errors you got from the "internal_labels" example, instead, I found a couple of missing taxa in the tree and a couple of wrong annotations. I now fixed the example and updated the repository. Many thanks for pointing out this problem.

About the real error you got from the "phylo_small" example, I looked into it, but here the example is working just fine. Could it be related to the matplotlib version? You mentioned the matplotlib warning, but I couldn't reproduce it. I am currently using the 1.3.1 version of matplotlib, which one are you using?

Instead of including PyPhlAn as sub-repository with GraPhlAn, I included the necessary classes directly in GraPhlAn. I also added a tag ("1.1", https://bitbucket.org/nsegata/graphlan/commits/tag/1.1) to the latest commit in Bitbucket.

Let us know if you have any other questions.
Many thanks,


On Fri, May 27, 2016 at 3:48 PM, Andreas Tille <andreas@fam-tille.de> wrote:
Sorry for answering my own mail.  When trying the examples of graphlan I
noticed that some files are missing:

graphlan/examples/guide $ ./step3.sh
Error: No tree file found: guide_2.xml
Error: No tree file found: guide_3.xml
Error: No tree file found: guide_3.xml

graphlan/examples/guide $ ./step4.sh
Error: No tree file found: guide_3.xml
Error: No tree file found: guide_4.xml
Error: No tree file found: guide_4.xml

I'm not sure about this, please check:

graphlan/examples/internal_labels $ ./step4.sh
Classes not implemented for external annotations
Classes not implemented for external annotations

I also observed two times warnings from matplotlib saying:

   /usr/lib/python2.7/dist-packages/matplotlib/projections/polar.py:149: RuntimeWarning: invalid value encountered in true_divide

A real error occures with

graphlan/examples/phylo_small $ ./run.sh
Traceback (most recent call last):
  File "/usr/bin/graphlan", line 70, in <module>
    external_legends = args['external_legends'])
  File "/usr/share/graphlan/src/graphlan_lib.py", line 1062, in draw
    format = out_format,
  File "/usr/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 577, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/figure.py", line 1470, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 2141, in print_figure
  File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 521, in print_png
  File "/usr/lib/python2.7/dist-packages/matplotlib/backends/backend_agg.py", line 469, in draw
  File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 59, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/figure.py", line 1079, in draw
  File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 59, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/axes/_base.py", line 2092, in draw
  File "/usr/lib/python2.7/dist-packages/matplotlib/artist.py", line 59, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/patches.py", line 462, in draw
  File "/usr/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 923, in set_alpha
  File "/usr/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 987, in set_foreground
    self._rgb = colors.colorConverter.to_rgba(fg, self._alpha)
  File "/usr/lib/python2.7/dist-packages/matplotlib/colors.py", line 376, in to_rgba
    'to_rgba: Invalid rgba arg "%s"\n%s' % (str(arg), exc))
ValueError: to_rgba: Invalid rgba arg "(0.0, 0.0, 1.0, 1.0175609756098)"
number in rbga sequence outside 0-1 range

BTW, a conversion to Python 3 for graphlan as well as pyphlan would be

Kind regards


On Fri, May 27, 2016 at 03:32:37PM +0200, Andreas Tille wrote:
> 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
>        Andreas.
> [1] https://bitbucket.org/nsegata/pyphlan
> [2] https://anonscm.debian.org/cgit/debian-med/python-pyphlan.git
> --
> http://fam-tille.de


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