[Debian-med-packaging] bedtools 2.26.0: new upstream release, problem with non-free material.

[Andreas Tille]

Hi Charles,

On Thu, Jul 07, 2016 at 02:05:35PM +0900, Charles Plessy wrote:
> >  
> > +  Problem: docs/content/images/tool-glyphs/barski_binding_site.png is from
> > +  Jothi et al, 2008, doi:10.1093/nar/gkn488, licensed under no-DFSG CC-BY-NC 2.0.
> > +
> > +  854dcc2 Merge tag 'v2.26.0' into debian/unstable
> 
> I wanted to update the bedtools package, but sorry, I do not have time to solve
> DFSG non-freeness issues with the documentation.  Please feel free to pick it up!

I'd suggest to just drop it from the doc via the following patch:

diff --git a/docs/content/tools/genomecov.rst b/docs/content/tools/genomecov.rst
index 2cad65e..1c33e2e 100755
--- a/docs/content/tools/genomecov.rst
+++ b/docs/content/tools/genomecov.rst
@@ -346,12 +346,6 @@ overlaps to be performed.
 Coverage by fragment
 ==============================================================================
 
-|
-
-.. image:: ../images/tool-glyphs/barski_binding_site.png
-
-|
-
 In ChiP-Seq the binding site is usually not at the coordinate where reads map,
 but in the middle of the fragment. For this reason we often try to estimate average fragment size
 for single-read experiment and extend the reads in the 5’-3’ direction up to the estimated fragment length.


and remove the image from the source tarball.  Unfortunately I have no
idea how to do this with the non-default repository structure.  What
do you think about the solution in general and do you have any advise
how to do this technically (except of turning the repository into a
default one :-P )

Kind regards

     Andreas.

-- 
http://fam-tille.de