[Blends-commit] r3146 - /projects/med/trunk/debian-med/tasks/bio

Sat Feb 18 18:08:30 UTC 2012

Author: tille
Date: Sat Feb 18 18:08:29 2012
New Revision: 3146

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3146
Log:
Delete more information about just uploaded packages

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3146&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sat Feb 18 18:08:29 2012
@@ -532,6 +532,14 @@
 Published-DOI: doi:10.1038/nbt.1621
 Published-URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
 Published-Year: 2010
+
+Suggests: eigensoft
+
+Depends: grinder
+
+Depends: jalview
+
+Depends: reprof
 
 Depends: axparafit
 Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
@@ -2283,18 +2291,6 @@
  and manipulation tool ATV and implementations of the SDI algorithm
  and the RIO method (http://www.phylosoft.org/).
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-
-Depends: jalview
-Homepage: http://www.jalview.org/
-License: GPL
-WNPP: 507436
-Responsible: Vincent Fourmond <fourmond at debian.org>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: multiple alignment editor
- Jalview is a multiple alignment editor written in Java. It is used
- widely in a variety of web pages (e.g. the EBI Clustalw server and
- the Pfam protein domain database) but is available as a general
- purpose alignment editor.
 
 Depends: lamarc
 Homepage: http://evolution.gs.washington.edu/lamarc/
@@ -3723,22 +3719,6 @@
  Transmission Disequilibrium Test TDT for family-based datasets and the
  chi-square test of association for case-control datasets.
 
-Suggests: eigensoft
-License: nonfree
-Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/eigensoft/trunk
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/eigensoft/trunk/
-Pkg-Description: reduction of population bias for genetic analyses
- The EIGENSOFT package combines functionality from the group's population
- genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
- method (Price et al. 2006). The EIGENSTRAT method uses principal components
- analysis to explicitly model ancestry differences between cases and
- controls along continuous axes of variation; the resulting correction is
- specific to a candidate marker's variation in frequency across ancestral
- populations, minimizing spurious associations while maximizing power to
- detect true associations. The EIGENSOFT package has a built-in plotting
- script and supports multiple file formats and quantitative phenotypes.
-
 Depends: sequenceconverter.app
 Homepage: http://bioinformatics.org/biococoa/
 License: GPL
@@ -3813,43 +3793,6 @@
  University of California, Berkeley Departments of Mathematics and
  Molecular and Cell Biology.
 
-Depends: reprof
-Responsible: Peter Hoenigschmid <hoenigschmid at rostlab.org>
-License: GPL-3
-WNPP: 655336
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/reprof/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/reprof/trunk/
-Homepage: http://rostlab.org/
-Pkg-Description: protein secondary structure and accessibility predictor
- 'reprof' is an improved implementation of 'prof', a popular protein secondary
- structure and accessibility predictor.  Prediction is either
- done from protein sequence alone or from an alignment - the latter should be
- used for optimal performance.
- .
- This package provides the 'reprof' command.  It is only a command line
- interface to the functionality provided by the modules in
- librg-reprof-bundle-perl.
-
-Depends: grinder
-Responsible: Florent Angly <florent.angly at gmail.com>
-Homepage: http://sourceforge.net/projects/biogrinder/
-Vcs-Git: git://git.debian.org/debian-med/grinder.git
-Vcs-Browser: http://git.debian.org/?p=debian-med/grinder.git
-License: GPL-3+
-Pkg-Description: Versatile omics shotgun and amplicon sequencing read simulator
- Grinder is a versatile program to create random shotgun and amplicon sequence
- libraries based on DNA, RNA or proteic reference sequences provided in a
- FASTA file.
- .
- Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,
- proteomic, metaproteomic shotgun and amplicon datasets from current
- sequencing technologies such as Sanger, 454, Illumina. These simulated
- datasets can be used to test the accuracy of bioinformatic tools under
- specific hypothesis, e.g. with or without sequencing errors, or with low or
- high community diversity. Grinder may also be used to help decide between
- alternative sequencing methods for a sequence-based project, e.g. should the
- library be paired-end or not, how many reads should be sequenced.
-
 Depends: hhsuite
 Homepage: http://toolkit.genzentrum.lmu.de/sections/search
 License: GPL-3.0+


