[Debichem-devel] [lopippo at users.alioth.debian.org: r4091 - /projects/debichem/trunk/debichem/tasks/polymer]

Fri Oct 31 19:22:52 UTC 2014

Hi,

I stumbled upon the latest commit of task polymer.

I would repeat my warning that the Published-* fields are *deprecated*
and at least in the four first cases (massxpert, mmass, lutefisk,
openms) totally unneeded since they are overriden by the data in

  debian/upstream/metadata

I have stopped checking whether debian/upstream/metadata exists for the
other packages.  Please do Published-* field whereever you find them in
tasks files and add a debian/upstream/metadata file instead in VCS (you
do *not* need to upload the according package to bring this in effect!)

Additional hint:  There is no point for users to install a package
featuring a dynamic library.  This comes as dependency of some
application.  The correct package to be specified here would be
libpwiz-tools.  It might make sense to add libpwiz-dev since this is
what a developer wants to install.

Hope these hints are helpful

      Andreas.

----- Forwarded message from lopippo at users.alioth.debian.org -----

Date: Fri, 31 Oct 2014 17:29:50 -0000
From: lopippo at users.alioth.debian.org
To: blends-commit at lists.alioth.debian.org
Subject: r4091 - /projects/debichem/trunk/debichem/tasks/polymer

Author: lopippo
Date: Fri Oct 31 17:29:49 2014
New Revision: 4091

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4091
Log:
Better documented the listed packages and added a bunch of new ones. Filippo Rusconi <lopippo at debian.org>.


Modified:
    projects/debichem/trunk/debichem/tasks/polymer

Modified: projects/debichem/trunk/debichem/tasks/polymer
URL: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/tasks/polymer?rev=4091&op=diff
==============================================================================

--- projects/debichem/trunk/debichem/tasks/polymer	(original)
+++ projects/debichem/trunk/debichem/tasks/polymer	Fri Oct 31 17:29:49 2014
@@ -1,15 +1,60 @@
 Task: Polymer editors and mass spectrometry
-Description: DebiChem polymer sequence editors and mass spectrometry
- This metapackage will install packages which enable you to edit
- polymer sequences so as to perform mass spectrometry simulations and
- view mass spectra.
-
+Description: DebiChem Analytical BioChemistry
+ This metapackage will install packages which enable you to:
+ .
+ - load and convert mass spectrometric data files;
+ - edit biopolymer sequences;
+ - elaborate complex mass spectrometry workflows;
+ - perform protein database searches using tandem-ms data;
+ - view and mine mass spectrometric data;
+ .
 
 Depends: massxpert
+Published-Title: massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data
+Published-Authors: F. Rusconi
+Published-In: Bioinformatics 25(20):2741-2742
+Published-URL: http://bioinformatics.oxfordjournals.org/content/25/20/2741
 
 Depends: mmass
+Published-Title: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data
+Published-Authors: M. Strohalm, D. Kavan, P. Novak, M. Volny and V. Havlicek
+Published-In: Anal. Chem. 82(11):4648-4651
 
 Depends: lutefisk
+Published-Title: Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry
+Published-Authors: R. S. Johnson and J. A. Taylor
+Published-In: Mol. Biotechnology Vol. 22, No. 3. (November 2002), pp. 301-315.
+
+Depends: openms
+Published-Title: OpenMS â€“ an Open-Source Software Framework  for  Mass  Spectrometry
+Published-Authors: Marc Sturm, Andreas Bertsch, Clemens GrÃ¶pl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher
+Published-In: BMC Bioinformatics, 9:163. doi:10.1186/1471-2105-9-163.
+
+Depends: libpwiz3
+Published-Title: A cross-platform toolkit for mass spectrometry and proteomics.
+Published-Authors: Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C.,  Creasy,  D.,  Flashner, L.,  Kani,  K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P.
+Published-In: Nature Biotechnology, 30. 10.1038/nbt.2377 (2012).
+
+Depends: python-mzml
+Published-Title: pymzML - Python module for high throughput bioinformatics on mass spectrometry data
+Published-Authors: T. Bald and J. Barth and A. Niehues and M. Specht and M. Hippler and C. Fufezan
+Published-In: Bioinformatics, UK, 28 (7), 1052-1053 (2012).
+
+Depends: tandem-mass
+Published-Title: Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system.
+Published-Authors: Peter Bowden and Ron Beavis and John Marshall
+Published-In: Journal of proteomics, 73 (1), 103-111 (2009)
+
+Depends: r-cran-maldiquant
+Published-Title: MALDIquant: a versatile R package for the analysis of mass spectrometry data
+Published-Authors: Gibb, Sebastian and Strimmer, Korbinian
+Published-In: Bioinformatics, 17 (28), 2270-2271 (2012)
+
+Depends: r-cran-maldiquantforeign
+
+Depends: r-cran-readbrukerflexdata
+
+Depends: r-cran-readmzxmldata
 
 Depends: biceps
 


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