[Debian-med-packaging] RFS: codonw

[Sascha Steinbiss]

Hi Andreas,

thanks for your feedback.

>>> 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.

Sure, no problem.

> 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

I see. This is really unfortunate.

[…]
> 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).

Well, these ‘tools’ are only symlinks to the main executable causing it to behave differently when called via the link. The functionality is also available using command line switches in the main codonw executable. Do you think it would be acceptable to drop or rename (e.g. codonw-cai, codonw-tidy, etc.) the linked tools? This would be my preference but could probably break existing third party scripts.

> I think upstream (if active currently) should made be
> aware about this conflict.

I can contact them and bring it up.

Cheers
Sascha