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

[Olivier Sallou]

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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
>
>
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> Debian-med-packaging at lists.alioth.debian.org
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- -- 
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)
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