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

[Aaron M. Ucko]

Andreas Tille <tille at debian.org> writes:

> I'm aware that language extensions in Debian are not conform to
> policy.  However, as we discussed in
>
>   https://lists.debian.org/debian-med/2018/06/msg00043.html
>
> only stripping the extension is sometimes hard for rdepends of
> our packages.  In this case the lack of blastpgp.pl requires
> heavy patching of t-coffee which could be avoided if we would
> provide both versions - blastpgp.pl and blastpgp - one of both
> as symlink.

Hi, Andreas.

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.)

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.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu