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

[Luca Capello]

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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