[Debian-med-packaging] Bug#642991: ncbi-blast+: should notify why some tools are missing

[Aaron M. Ucko]

Luca Capello <luca at pca.it> writes:

> Please note that I have never used any of the tools below, I am simply
> moving a lenny machine with manually-installed BLAST+ to squeeze with
> the Debian package ;-)

Nevertheless, I appreciate your suggestions.

> Some BLAST+ upstream tools are missing in the Debian package and I could
> not find the reason in the README.Debian.  According to the SVN log
> (thus something not really end-user), these are considered "tests,
> demos, and internal build tools":

As Olivier noted, BLAST+ is a subset of NCBI's C++ Toolkit; although we
have not yet managed to package the Toolkit in its entirety, we would
like to avoid adding extra hurdles to doing so.

>    From the upstream page above: "DATATOOL can be used to formally
>    convert any ASN.1 or XML data or data specification".  Given that you
>    can download ASN.1 sequences directly from upstream NCBI, IMHO this
>    should be included in the binary package.

datatool certainly has its uses, but it is nevertheless somewhat beyond
the scope of the ncbi-blast+ binary package.  As such, if we are to ship
it, I'd favor splitting it out into its own package (taking the
opportunity to supply a suitable version number) and doing the same for
the handful of private shared libraries it needs.

>    BTW, is the ucko in the commit logs for gene_info.cpp the same Aaron
>    M. Ucko working on the Debian package?  In this case, he knows better
>    than me ;-)

I am, but hadn't noticed that gene_info_reader, unlike the vast majority
of the Toolkit's demos, may actually be of interest to end users, not
just developers; I'm open to including it in the ncbi-blast+ binary
package.

> 3) project_tree_builder
>    <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/project_tree_builder/>
>
>    Used to generate makefiles, internal, not needed.

Indeed.

Thanks for the feedback!

(Olivier, please let me know if you'd like help implementing any of
those suggestions.)

-- 
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