-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi, 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.
Some other tools, though coming from the same origin, could be included in an other package (tools) Olivier Le 9/26/11 12:54 PM, Luca Capello a écrit : > Package: ncbi-blast+ > Version: 2.2.25-5 > Severity: normal > Usertags: unige-jmlab > > Hi there! > > 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 ;-) > > 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": > > <http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/debian/rules?revision=6880&view=markup> > > 1) datatool > <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/datatool/> > <http://www.ncbi.nlm.nih.gov/data_specs/NCBI_data_conversion.html> > > 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. > > 2) gene_info_reader > <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objtools/blast/gene_info_reader/> > > From its -h output: "the program can be used to convert Gene IDs > to/from Gis, and print Gene Info lines given Gis or Gene IDs". This > does not seem to me an internal tool at all. > > However, the CLI is actually the application from the demo subfolder, > but IMHO still worth inclusion. > > 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 ;-) > > 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. > > Thx, bye, > Gismo / Luca > > -- System Information: > Debian Release: wheezy/sid > APT prefers unstable > APT policy: (500, 'unstable') > Architecture: amd64 (x86_64) > > Kernel: Linux 3.1.0-rc4-amd64 (SMP w/2 CPU cores) > Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) (ignored: LC_ALL set to C) > Shell: /bin/sh linked to /bin/dash > > Versions of packages ncbi-blast+ depends on: > ii libbz2-1.0 1.0.5-7 > ii libc6 2.13-21 > ii libgcc1 1:4.6.1-12 > ii libpcre3 8.12-4 > ii libstdc++6 4.6.1-12 > ii ncbi-data 6.1.20110713-1 > ii perl 5.12.4-4 > ii python 2.6.7-3 > ii zlib1g 1:1.2.3.4.dfsg-3 > > ncbi-blast+ recommends no packages. > > ncbi-blast+ suggests no packages. > > -- no debconf information > > > _______________________________________________ > Debian-med-packaging mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging - -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iQIcBAEBCAAGBQJOgGAgAAoJEHjcaNsybYQ40t0P/R0pEHpyvVz5G+eWiaU88aRP ci4mrMrtPXkaxK8m77f4XbKU6PJr4xyfrD3oTJVdLGwaz9kihnDd3LFlIuUqjGLC ZV++ggky4G54/9gVWX9xkpHKYA/NunotzPS84reTVsbOujMuE+gHRunanQ8i3BwT 75NalMp5mDIUz9JLabOp2M1nzHw+kiZQo2NOSzoVlmNAiGqKupmNirP6i/VCHj1C 64AHSk50T52xUrFqq3XKPDf4t4w6QwXxbqLZgykgfxkssBm4GABMKeHLpB9StdDc ffXCvreTNv++on61AOgY8hwSwsbPZgr3vo4FsLsG+gGllRLkMZJekHvMNwgq9TMj MBkI5zbE8ToTvWWTvL1UBEh6AoFxs+MAT8n2wwOObS9gc0nL+QW/PrbwQC+BQ3OY eeZQe0HhAsbdT6sga0ZrekTrflcF8tNmbSVIASGD2Nk3y4gvbj9ZeYngyy4GJ3d+ WWVVE/pVLT7IuZrABKymuv0MUbll7SQr+IQgpttUvZ1UoAVUDDL6gAF9OuDNlK3c QQh2CMvtzMYu1u3VsyDijYVYHAbk4uaO2LyMZTtDZhATtMjl07YK0mFRimBeEMVG aQAWJFuK1/5QX/Ye961mbtjs3sPdjphfQO54ZLY30whr4sDgMx5lvhUNijhhWJnx 74iDiA+viG8II4V9jD1C =VeNB -----END PGP SIGNATURE-----
