Hi there! Cc:ing the debian-med@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@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
Attachment:
pgp6GnneKppJw.pgp
Description: PGP signature