[Blends-commit] r1420 - projects/med/trunk/debian-med/tasks

Sun Mar 8 06:41:47 UTC 2009

Author: plessy
Date: Sun Mar  8 06:41:47 2009
New Revision: 1420
URL: http://svn.debian.org/viewsvn/blends?rev=1420&view=rev

Log:
Grouped some programs in broader categories.


Modified:
   projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=1420&view=diff&r1=1420&r2=1419&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Sun Mar  8 06:41:47 2009
@@ -9,20 +9,26 @@
 Depends:     molphy, phylip, treetool
 Why:         Phylogenetic analysis (Non-free, thus only suggested).
 
-Depends:     fastlink, loki, r-cran-qtl
+Depends:     fastlink, loki, plink, r-cran-qtl
 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
+Depends:     amap-align, blast2, boxshade, dialign, dialign-tx, gff2aplot, hmmer, kalign, mafft, mummer, muscle, poa, probcons, proda, seaview, sim4, sibsim4, sigma-align, t-coffee, wise, exonerate
 Why:         Sequence alignments and related programs.
 
-Depends:     embassy-domalign, embassy-domainatrix
+Depends:     last-align, maq, ssake, velvet
+Why:         Tools related to high-throughput sequencing.
 
+Depends:     emboss, embassy-domalign, embassy-domainatrix
 Suggests:    emboss-explorer
+Why:         The EMBOSS sequence analysis suite and its galaxy.
 
 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, r-other-bio3d
+Depends:     infernal, rnahybrid.
+Why:         For the analysis of RNA sequences.
+
+Depends:     adun.app, garlic, gamgi, gdpc, ghemical, gromacs, pymol, rasmol, autodock, autogrid, r-other-bio3d
 Why:         Molecular modelling and molecular dynamics.
 Comment:     r-other-bio3d depends from r-cran-rocr which is also maintained by Debian Med team
 
@@ -35,31 +41,19 @@
 Suggests:    mozilla-biofox
 Why:         Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user.
 
-Depends: dialign-tx
-
 Depends: glam2
 Why:         Motif search
 
-Depends: mafft, rnahybrid
-
-Depends: last-align
-
 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
      work under Mac OSX only and it is not really maintained (Debian QA group).
      We want to keep track of it anyway.
 
-Depends: maq
-
 Depends: raster3d
 
-Depends: plink
-
 Depends: autodocktools
 
-Depends: gamgi
-
 Depends: mgltools-dejavu, mgltools-pmv, mgltools-utpackages, mgltools-vision, mgltools-volume
 Comment: The package autodocktools depends from the mgltools-* packages mentioned
          above, so they will be installed even if they would not be mentioned in
@@ -79,10 +73,6 @@
 
 Depends: theseus
 
-Depends: ssake
-
-Depends: velvet
-
 Depends: pdb2pqr
 Homepage: http://pdb2pqr.sourceforge.net/
 Responsible: Manuel Prinz <debian at pinguinkiste.de>
@@ -299,28 +289,6 @@
  Citation: Population dynamics of HIV-1 inferred from gene sequences
  Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.
 
-Depends: infernal
-Homepage: http://infernal.janelia.org/
-Responsible: Steffen Moeller <moeller at debian.org>
-License: GPL
-WNPP: 441840
-Pkg-URL: http://packages.debian.org/source/experimental/infernal
-Pkg-Description: RNA sequence comparison
- Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
- databases for RNA structure and sequence similarities. It is an
- implementation of a special case of profile stochastic context-free
- grammars called covariance models (CMs). A CM is like a sequence
- profile, but it scores a combination of sequence consensus and RNA
- secondary structure consensus, so in many cases, it is more capable of
- identifying RNA homologs that conserve their secondary structure more
- than their primary sequence.
- .
- The tool is an integral component of the Rfam database.
- .
- Users of this package should cite:
- "Query-Dependent Banding (QDB) for Faster RNA Similarity Searches."
-  E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007.
-
 Depends: asap
 Homepage: http://asap.ahabs.wisc.edu/software/asap/
 Responsible: Andreas Tille <tille at debian.org>

