[Debian-med-packaging] Bug#956850: Bug#956848: ncbi-blast+-legacy: Please provide /usr/bin/blastpgp.pl (including .pl extension)

[Andreas Tille]

Hi Aaron,

On Fri, Apr 17, 2020 at 06:58:12PM -0400, Aaron M. Ucko wrote:
> 
> I'm open to making these changes if necessary, particularly given that
> this directive is merely a "should" and that there's a fair bit of
> precedent for violating it.  (Also, ncbi-blast+ will need a new upload
> anyway to address a formal GCC 10 recognition issue, per #957581.)

Thanks a lot.
 
> However, on the t-coffee side, I'd like to offer some alternatives to
> this heavy patching:
> - Have debian/rules automatically make this formal change in
>   a new override_dh_configure target and revert it in
>   override_dh_clean.
> - Ship a private directory (say, /usr/share/t-coffee/bin) containing
>   symlinks or wrappers with .pl extensions and arrange to add it to PATH
>   at launch.
> - Better yet, bypass these scripts and run BLAST+ directly; they even
>   offer a --print_only flag that helps with such porting.
> 
> Thanks for maintaining t-coffee (and so many other packages), and please
> let me know if any of these suggestions works for you.

I agree that all three of your suggestions are probably way better than
the error prone patching.  I simply continued to do what was done before
and those few times I need to do its just a tiny bit below to do a real
change. ;-)  However, besides t-coffee I think that are probably more
tools around which are expecting the .pl extensions on those prominent
tools from ncbi-blast.

BTW, I do not understand your third suggestion ("Better yet ...").  It
seems you are proposing a real enhancement but I just don't get it.
Would you mind providing a patch for t-coffee implementing this?

Kind regards

     Andreas.

-- 
http://fam-tille.de