[Cdd-commits] r1023 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: moeller
Date: Sun Aug 10 12:02:04 2008
New Revision: 1023

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Two packages have arrived in main and grouped to the right "depends". Andreas has edited bio3d in parallel.



Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Sun Aug 10 12:02:04 2008
@@ -9,7 +9,7 @@
 Depends:     molphy, phylip, treetool
 Why:         Phylogenetic analysis (Non-free, thus only suggested).
 
-Depends:     fastlink, loki, r-cran-qtl
+Depends:     fastlink, loki, r-cran-qtl, r-other-genabel
 Why:         Genetics
 
 Depends:     amap-align, blast2, boxshade, dialign, gff2aplot, emboss, hmmer, kalign, mummer, muscle, poa, probcons, proda, seaview, sim4, sibsim4, sigma-align, t-coffee, wise, exonerate
@@ -18,7 +18,7 @@
 Depends:     arb, clustalw | clustalw-mpi, clustalx
 Why:         Sequence alignments and related programs (Non-free, thus only suggested).
 
-Depends:     adun.app, garlic, gdpc, ghemical, gromacs, pymol, rasmol, autodock, autogrid
+Depends:     adun.app, garlic, gdpc, ghemical, gromacs, pymol, rasmol, autodock, autogrid, r-other-bio3d
 Why:         Molecular modelling and molecular dynamics.
 
 Depends:     plasmidomics
@@ -33,11 +33,10 @@
 Depends: dialign-tx
 
 Depends: glam2
+Why:         Motif search
 
 Suggests: pdb2pqr
 
-Depends: r-other-bio3d
-
 Suggests: biococoa.app
 Why: Only suggests, because current version in Debian breaks, has new upstream -
      at least version 1.7 might run under Linux, the new designed 2.0 seems to
@@ -1938,37 +1937,6 @@
  during a pass through the model (the expected contribution).
  .
  If you use HMM-Logos in your publication, please cite HMM Logos for
- visualization of protein families.  Schuster-Böckler B, Schultz J,
+ visualization of protein families.  Schuster-B"ockler B, Schultz J,
  Rahmann S BMC Bioinformatics. 2004;5;7. PMID: 14736340 DOI:
  10.1186/1471-2105-5-7
-
-Depends: r-other-bio3d
-Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d
-Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-bio3d
-WNPP: 492499
-Responsible: Steffen Moeller <moeller at debian.org>
-Pkg-Description: GNU R package for biological structure analysis
- The bio3d package contains utilities to process, organize and explore
- protein structure, sequence and dynamics data.  Features include the
- ability to read and write structure, sequence and dynamic trajectory
- data, perform atom summaries, atom selection, re-orientation,
- superposition, rigid core identification, clustering, torsion analysis,
- distance matrix analysis, structure and sequence conservation analysis,
- and principal component analysis (PCA).  In addition, various utility
- functions are provided to enable the statistical and graphical power of
- the R environment to work with biological sequence and structural data.
-
-Depends: r-other-genabel
-Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL
-Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-genabel
-WNPP: 492044
-Responsible: Steffen Moeller <moeller at debian.org>
-Pkg-Description: GNU R package for genome-wide SNP association analysis
- The package offers the R library GenABEL for the hunt of genetic contributions
- to a disease (or any other pheonypical trait) by so called genome-wide
- association analysis. Additional input commonly comes from DNA mircoarray
- experiments, performed on every individual, that determine differences
- (polymorphisms) in the population. GenABEL finds associations between
- quantitative or binary traits and single-nucleiotide polymorphisms
- (SNPs). 
-