Re: igblast accepted - how can it be used to test igdiscover

["Aaron M. Ucko" <ucko@debian.org>]

Andreas Tille <andreas@an3as.eu> writes:

> into igdiscover changelog.  Igblast is accepted now.  However, despite I did
> the final upload I did not checked for actual binaries which are all "hidden"
> in usr/lib/ncbi-igblast/bin.  I simply took over your and David's packaging
> layout and cared that it builds latest upstream.

Thanks for taking IgBLAST on in general.  This packaging is off to a
good start, but I'm sorry to say still not quite right.  In particular:

- The executables to build and install directly are igblastn and
  igblastp along with the edit_imgt_file.pl script (which Policy 10.4
  says should be installed without its extension, though I know that's
  somewhat controversial within this team).  All come from app/igblast
  and should in fact wind up in /usr/bin.

- As for other executables, supporting tools can and should come from
  ncbi-blast+ (for which I reckon a Recommends should suffice) and you
  don't need to install tests at all.

- Because you're installing multiple binaries (even if fewer than at
  present), building supporting libraries dynamically should save space;
  please see ncbi-blast+ for an illustration of how to do so and
  subsequently install only those shared libraries you'll actually need
  at runtime.  To avoid possible skew or missed IgBLAST-specific
  tuneups, it's probably best for the IgBLAST packaging to supply its
  own versions of these files, rather than building against libraries
  from ncbi-blast+ once a corresponding development package happens.
  (I realize that this approach goes against policy, but the libraries
  in question are at least generally native to both source bases.)

- Some use cases may want app/igblast's internal_data and optional_file
  subtrees, which I'd suggest installing to /usr/share/ncbi/igblast; I
  can adjust the ncbi-data package to facilitate finding those subtrees
  there.

- The package FTBFS on some architectures.  Future releases should do
  better, at least on those specific fronts, but meanwhile you might
  want to copy some patches from ncbi-blast+.

Thanks again, and please let me know if you'd like further advice on any
of those fronts.  Also, sorry for not offering concrete patches; I'm
already spread a bit too thin.

-- 
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