[Blends-commit] r2962 - in /projects/med/trunk/debian-med/tasks: bio bio-phylogeny

Sun Oct 2 06:07:49 UTC 2011

Author: tille
Date: Sun Oct  2 06:07:48 2011
New Revision: 2962

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2962
Log:
More removals of redundant information

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2962&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sun Oct  2 06:07:48 2011
@@ -3008,6 +3008,18 @@
 
 Depends: populations
 
+Depends: raccoon
+
+Depends: snap
+Published-Authors: I. Korf
+Published-Title: Gene finding in novel Genomes
+Published-In: BMC Bioinformatics
+Published-DOI: doi:10.1186/1471-2105-5-59
+Published-URL: http://www.biomedcentral.com/1471-2105/5/59/abstract
+Published-Year: 2004
+
+Depends: vcftools
+
 Depends: denoiser
 WNPP: 587274
 Homepage:  http://www.microbio.me/denoiser/
@@ -3366,21 +3378,6 @@
  projects. In consequence, there is a dramatic increase in the volume of
  sequence data to be analyzed.
 
-Depends: vcftools
-Homepage: http://vcftools.sourceforge.net/
-License: GPLv3
-WNPP: 633142
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/vcftools/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/vcftools/trunk
-Pkg-Description: validating, merging, comparing and calculate some basic population genetic statistics
- VCFtools is a program package designed for working with VCF files, such
- as those generated by the 1000 Genomes Project. The aim of VCFtools is
- to provide methods for working with VCF files: validating, merging,
- comparing and calculate some basic population genetic statistics.
-Remark: Packaging requested by BIOLINUX
- This package is listed at http://www.bioinformatics.org/wiki/BIOLINUX to
- be quite important for BIOLINUX.
-
 Depends: ray-denovoassembler
 Homepage: http://sourceforge.net/projects/denovoassembler/
 License: GPLv3
@@ -3428,23 +3425,6 @@
  contigs and BACs without the overhead of a database. MAKER should prove
  especially useful for emerging model organism projects with minimal
  bioinformatics expertise and computer resources
-
-Depends: snap
-Homepage: http://homepage.mac.com/iankorf/
-License: GPL2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/snap/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/snap/trunk/
-WNPP: 630753
-Pkg-Description: location of genes from DNA sequence with hidden markov model
- SNAP is a general purpose gene finding program suitable for both eukaryotic
- and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid
- Parser.
-Published-Authors: I. Korf
-Published-Title: Gene finding in novel Genomes
-Published-In: BMC Bioinformatics
-Published-DOI: doi:10.1186/1471-2105-5-59
-Published-URL: http://www.biomedcentral.com/1471-2105/5/59/abstract
-Published-Year: 2004
 
 Depends: repeatmasker
 Homepage: http://www.repeatmasker.org/
@@ -3686,32 +3666,6 @@
  of data visualization, exploration, preprocessing and modeling
  techniques. It can be used through a nice and intuitive user interface
  or, for more advanced users, as a module for Python programming language.
-
-Depends: raccoon
-Homepage: http://autodock.scripps.edu/resources/raccoon
-WNPP: 630977
-License: GPL-3.0+
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/raccoon/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/raccoon/trunk/
-Pkg-Description: preparation of in silico drug screening projects
- The field of computational biology is all about modeling
- physiochemical entities. Structural biology is about how
- those entities look in 3D and behave. And we have a drug
- when we can change that behaviour in a way that we want it
- to be changed - and only that behaviour.
- .
- Some good part of the characterisation of promising
- drug-like compounds for their interaction with a larger protein
- can be done on computers. This package helps with getting
- collections of small ligands prepared to be fitted against
- a particular protein of known structure. That docking itself
- is then to be performed by autodock or autodock-vina.
- .
- Raccoon may not find the drug, but it may well find a
- lead to it. To have this package with Debian shall help
- smaller biochemistry labs and grants an opportunity for the
- general public to educate itself and/or actively join in to
- help the world .... just a bit.
 
 Depends: python-reaper
 Homepage: http://qtlreaper.sf.net

Modified: projects/med/trunk/debian-med/tasks/bio-phylogeny
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-phylogeny?rev=2962&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-phylogeny (original)
+++ projects/med/trunk/debian-med/tasks/bio-phylogeny Sun Oct  2 06:07:48 2011
@@ -250,23 +250,6 @@
  gBioSeq is in an early stage of development, but it is already running.
  The goal is to provide an easy to use software to edit DNA sequences under
  Linux, Windows, MacOsX, using GTK C# (Mono).
-
-Depends: populations
-Homepage: http://bioinformatics.org/~tryphon/populations/
-License: GPL
-Pkg-Description: individuals or populations distances based on allelic frequencies
- Population genetic software (individuals or populations distances, phylogenetic trees)
-  * haploids, diploids or polyploids genotypes (see input formats)
-  * structured populations (see input files structured populations
-  * No limit of populations, loci, alleles per loci (see input formats)
-  * Distances between individuals (15 different methods)
-  * Distances between populations (15 methods)
-  * Bootstraps on loci OR individuals
-  * Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA
-    (PHYLIP tree format)
-  * Allelic diversity
-  * Converts data files from Genepop to different formats (Genepop, Genetix, Msat,
-    Populations...)
 
 Depends: phpphylotree
 Homepage: http://www.bioinformatics.org/project/?group_id=372


