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

Tue Sep 27 13:42:08 UTC 2011

Hi there!

Cc:ing the debian-med at l.d.o mailing list.  Please Cc: me on replies, I
am not subscribed to the list nor to the bug.

For #642986 (Bcc:ed): the relevant part is point 1) below.

On Mon, 26 Sep 2011 20:23:55 +0200, Aaron M. Ucko wrote:
> 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.

I am sorry, I should have written that "I have never used any of the
tools below *on Debian*": FYI I am a molecular biologist working with
BLAST since 2002, so I know something about these programs ;-)

>> 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,

Olivier, can you please Cc: the bug submitter in your replies, if not
stated differently?

> 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.

Which I understand.

On Mon, 26 Sep 2011 13:21:05 +0200, Olivier Sallou wrote:
> indeed, some tools are not considered as stable though included in same
> trunk. In fact, all are not really "Blast" related.
> All comes from a ncbi-tools package, which include many tools and common
> libs.
> The ncbi-blast+ package only includes the blast related software.

I am sorry, but what you wrote is not completely correct:

a) the ncbi-blast+ package correspond to upstream ncbi-blast-$VERSION+,
   not to the upstream ncbi-tools:
=====
$ wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--7_0_0.tar.gz
[...]
2011-09-27 15:03:00 (3.62 MB/s) - `ncbi_cxx--7_0_0.tar.gz' saved [18400662]

$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-src.tar.gz
[...]
2011-09-27 15:00:45 (2.76 MB/s) - `ncbi-blast-2.2.25+-src.tar.gz' saved [11923391]

$ apt-get source ncbi-blast+
[...]
Fetched 11.9 MB in 4s (2,974 kB/s)
dpkg-source: info: extracting ncbi-blast+ in ncbi-blast+-2.2.25
dpkg-source: info: unpacking ncbi-blast+_2.2.25.orig.tar.gz
dpkg-source: info: unpacking ncbi-blast+_2.2.25-5.debian.tar.gz
dpkg-source: info: applying hurd_fixes
dpkg-source: info: applying legacy_rename_rpsblast
dpkg-source: info: applying fix_checks
dpkg-source: info: applying fix_gcc46_errors
dpkg-source: info: applying support_other_cpus
dpkg-source: info: applying fix_lib_deps
dpkg-source: info: applying no_multiarch_rpath

$ md5sum ncbi_cxx--7_0_0.tar.gz ncbi-blast-2.2.25+-src.tar.gz ncbi-blast+_2.2.25.orig.tar.gz
f7ac868f3b71f81c2a22b3210e5eecc6  ncbi_cxx--7_0_0.tar.gz
01256b808e3af49a5087945b6a8c8293  ncbi-blast-2.2.25+-src.tar.gz
01256b808e3af49a5087945b6a8c8293  ncbi-blast+_2.2.25.orig.tar.gz
=====

b) the upstream ncbi-blast+ package contains the three binaries I
   spotted in my first email (datatool, gene_info_reader and
   project_tree_builder), ergo they belong to the Debian ncbi-blast+
   *source* package (as it is now).

c) I see nowhere that some tools are not considered stable, I would say
   the contrary instead:

     <http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews>

     BLAST 2.2.25 release

     Thu, 24 Mar 2011 09:00:00 EST

     A new version of the stand-alone applications is available.
     Users are encouraged to use the BLAST+ applications available at
     ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ This
     release includes a substantial number of bug fixes and new features
     for the BLAST+ applications.

On Mon, 26 Sep 2011 20:23:55 +0200, Aaron M. Ucko wrote:
> 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.

See at the end.

>>    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.

See at the end.

On Tue, 27 Sep 2011 09:18:13 +0200, Olivier Sallou wrote:
> according to the previous discussions, I suggest to move the bug to
> wishlist severity:

I disagree, but it is your call.

> 1) people seem to agree that we should not modify extensions from upstream

Where does this come from?  It has nothing to do with this bug and I
guess you are referring to:

  <http://lists.debian.org/20110926100704.GD3361%40merveille.plessy.net>

It is funny how the guy who started the discussion (see #642986) is not
notified of subsequent actions about such a discussion...  And, before
any change in how the Debian Med people package software, please consult
debian-devel@, as Andreas suggested:

  <http://lists.debian.org/20110927061903.GF29016%40an3as.eu>

However, in this specific case, I think the path is already clear:

  <http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=190753#118>

Please reply to this specific topic removing the bug report or, if you
prefer, adding #642986.  If you really want my opinion, read Don's:

  <http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=190753#75>

> 2) other tools that could be usefull should be splitted to an other packet.

Again, I disagree.

Please note that I do not care where these tools end up, but if they are
shipped with ncbi-blast+ *and* you keep the same source as upstream,
they I would say that installing a Debian ncbi-blast+ package should
include all upstream tools for consistency (and simplicity).  Or, in
case you want to remove/split something, then this should be well
documented (which is why I reported this bug in primis).

Sometime excessive splitting is bad, which is what I think WRT the
ncbi-blast+-legacy package: an extra 6.6KB package for a single 65B
shell script is IMHO useless, especially when the non-legacy package
already ships with a legacy script (see also #642986).

Thx, bye,
Gismo / Luca
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