[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

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

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


Reply to: