[Debian-med-packaging] RFS: codonw

[Andreas Tille]

Hi Sascha,

On Sat, Nov 21, 2015 at 11:42:37PM +0000, Sascha Steinbiss wrote:
> > 
> > Yes, it is not the most beautiful solution. I can write short individual man pages for each of the tools which simply state that these are basically just shortcuts selecting one particular analysis option in the main codonw executable.
> 
> I have now added individual man pages and also some other documentation.

Cool - you have spent a certain amount of work into this.  Thanks for
doing so.

Unfortunately I spotted another problem which might be harder to solve.
We are now diving into name space conflicts even *inside* the Debian Med
scope (see first hit emboss:

apt-file search /usr/bin/cai | grep cai$
emboss: /usr/bin/cai

pt-file search /usr/bin/cu | grep cu$
cu: /usr/bin/cu

apt-file search /usr/bin/fop | grep fop$
fop: /usr/bin/fop

apt-file search /usr/bin/gc | grep gc$
graphviz: /usr/bin/gc

apt-file search /usr/bin/tidy | grep tidy$
tidy: /usr/bin/tidy


To avoid conflicts with five packages we need to move the tools to
/usr/lib/codonw and provide a wrapper script (as an example see the
phylip package).  While I usually suggest as an alternative for Debian
Med users to use a specific binary dir prepended to the PATH of Debian
Med users (see plink package) this would be problematic when users want
to use emboss.  I think upstream (if active currently) should made be
aware about this conflict.

Kind regards

        Andreas.

-- 
http://fam-tille.de