[Debian-med-packaging] Emperor (Was: Patch for ampliconoise)

[Tim Booth]

Hi Andreas,

I've tested my new QIIME package with my Emperor package and confirmed
that nice 3D interactive graphs can be viewed in Firefox after running
beta_diversity_through_plots.py in QIIME which calls make_emperor.py.

My inclination for Bio-Linux is to put this out as it is now (with all
the embedded JS), because I can't be sure that replacing the JS
libraries with different versions will not cause problems and in any
case the versions you have on Sid are going to be much newer than
Precise (only 2 months to the next LTS release).

Once we have the new Ubuntu release and hopefully a v1 release of
Emperor I think that will be a better time to try out a deconstructed
version of the package.

Cheers,

TIM

On Thu, 2014-02-27 at 08:57 +0000, Andreas Tille wrote:
> Hi Tim,
> 
> I have replaced some of the JS libraries by their Debian packaged
> version.  I'd regard my way a bit hackish since the links pretend to be
> some versions but they are more up to date.  Perhaps it is better / more
> clear to patch the upstream source.
> 
> Besides this detail I would like to hear your opinion about the current
> state in SVN.  Does it work under your target distribution?  Should we
> go on with this approach or do you suggest any other plan?
> 
> Kind regards
> 
>         Andreas.
> 
> On Tue, Feb 25, 2014 at 04:54:20PM +0100, Andreas Tille wrote:
> > Hi Tim,
> > 
> > On Tue, Feb 25, 2014 at 02:47:16PM +0000, Tim Booth wrote:
> > > > Cool!  I just noticed your commits and did some first steps into getting
> > > > it straight into Debian.  I'm a bit worried about the JS files which are
> > > > considered as "binary without source" by ftpmaster.  I'll see what I can
> > > > do to relax the situation.
> > > 
> > > I'd be inclined to agree with ftpmaster on this one, as packed JS is
> > > virtually unhackable, but if you look through the various JS files here
> > > most are in unpacked form, plus all the sources are listed in LICENCE.md
> > > so it would be doable to make this DFSG compliant.
> > 
> > I agree that I might have been a bit exaggerated and perhaps the
> > situation is not as bad as expected (I just had a quick look when I
> > wrote the mail above.  I think we could definitely get rid of the
> > suspicious file
> > 
> >    doc/files/files.zip
> > 
> > It is only used in the tutorial and I patched it to download the file
> > from web rather than having a local copy.  This will save us from some
> > copyright discussion and a rarely used space consuming file (IMHO, feel
> > free to disagree).
> > 
> > Once I was starting to remove files I also have removed the code copy of
> > libjs-twitter-bootstrap.  Please verify that your target distribution
> > will include this Build-Dependency (as well as dh-linktree!).  If this
> > might cause you trouble we can revert the removal and do some
> > conditional build.
> > 
> > > Unfortunately it
> > > does mean packaging lots of little scraps off GitHub and there is no
> > > saying if different versions of the JS will be compatible.
> > > 
> > > It raises the question - should a package like this be "compiled" by
> > > packing all the JS at build time?  Are you aware of any packages that do
> > > this?
> > 
> > Once I had to deal with an RC bug in gnumed-client where it was
> > sufficient to provide the JS sources in the debian/ dir in addition to
> > what upstream provides.  There is no need to work down all the stuff by
> > separate packages
> > 
> > > Anyway, for now I just want to try and get things working.
> > 
> > I will have a deeper look and let you know.
> > 
> > Kind regards
> > 
> >       Andreas.
> > 
> > -- 
> > http://fam-tille.de
> > 
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> > 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
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