[Debichem-devel] Please maintain DebiChem tasks files [Was: Bug#693800: ITP: tandem-mass -- mass spectrometry software for protein identification]

[Andreas Tille]

Hi,

you might know (or at least assume) that I'm closely watching ITPs and
whether the packages finally make their way into the relevant tasks.
The one below was even uploaded to Debian but not yet included into any
of the DebiChem tasks ... but should.

I have no idea whether you are aware that you can even

    Depends: not_yet_uploaded_file_in_vcs

so actually in most cases after issuing an ITP bug it makes sense to
include the package into a task (no, we do not *yet* parse ITP bugs,
but I simply assume that the package might be at this time in VCS or
at least will show up there soonish.)  This helps drastically to not
forget maintaining the tasks files.

I have not yet checked other chemestry relevant ITPs or whether all
packages relevant for DebiChem are mentioned in the tasks files but I
would like to explicitely mention that there is the chance to get
changes een into Wheezy as I informed the release team about the
to be expected changes[1].

It even might be possible to add new tasks that might be missing
currently however, I would like to add a *big* *warning* *against*
*renaming* of any metapackage compared to the current metapackages
in testing.  Currently the blends-dev framework does not have some
means to add the needed "Replaces/Conflicts/Provides" magic that
would be needed - so I was falling into this trap once and I only
can recommend to stay away from any renamings for now.

In short:  Please maintain the DebiChem tasks right now to get it
updated in Wheezy and add all missing Dependencies (and possibly new
tasks.)

Kind regards

      Andreas.

[1] http://lists.debian.org/debian-release/2012/06/msg00323.html

----- Forwarded message from Olivier Langella <Olivier.Langella at laposte.net> -----

Date: Tue, 20 Nov 2012 14:58:02 +0100
From: Olivier Langella <Olivier.Langella at laposte.net>
To: Debian Bug Tracking System <submit at bugs.debian.org>
Subject:  Bug#693800: ITP: tandem-mass -- mass spectrometry software for protein identification

Package: wnpp
Severity: wishlist
Owner: Olivier Langella <Olivier.Langella at laposte.net>


* Package name    : tandem-mass
  Version         : 20121001
  Upstream Author : The Global Proteome Machine Organization
* URL             : http://www.thegpm.org/TANDEM/
* License         : Artistic License 1.0
  Programming Lang: C++
  Description     : mass spectrometry software for protein identification

 X! Tandem can match tandem mass spectra with peptide sequences, in a
 process that is commonly used to perform protein identification.
 .
 This software has a very simple, unsophisticated application
 programming interface (API): it simply takes an XML file of
 instructions on its command line, and outputs the results into an XML
 file, which has been specified in the input XML file. The output file
 format is described at
 \fI`http://www.thegpm.org/docs/X_series_output_form.pdf'\fR.
 .
 Unlike some earlier generation search engines, all of the X! Series
 search engines calculate statistical confidence (expectation values)
 for all of the individual spectrum-to-sequence assignments. They also
 reassemble all of the peptide assignments in a data set onto the
 known protein sequences and assign the statistical confidence that
 this assembly and alignment is non-random. The formula for which can
 be found here. Therefore, separate assembly and statistical analysis
 software, e.g. PeptideProphet and ProteinProphet, do not need to be
 used.


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