[Blends-commit] r2961 - in /projects/med/trunk/debian-med/tasks: bio bio-phylogeny

tille at users.alioth.debian.org tille at users.alioth.debian.org
Sun Oct 2 06:01:37 UTC 2011 

Author: tille
Date: Sun Oct  2 06:01:36 2011
New Revision: 2961

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2961
Log:
Removed some extra information about now officially available packages

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=2961&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sun Oct  2 06:01:36 2011
@@ -183,7 +183,7 @@
  not possible to specify an "OR relation" and tag the Published-* fields to only one
  of them.
 
-Depends: mothur, bowtie
+Depends: mothur, bowtie, dotur
 
 Depends: transtermhp
 
@@ -1078,24 +1078,6 @@
  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-URL: https://launchpad.net/~olivier-langella/+archive/ppa/+packages
-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
@@ -2161,27 +2143,6 @@
 Comment: BioLinux contains a dendroscope package which is available
  at http://www.dendroscope.org but this project has only a
  "free as in beer" binary download - so this is not for us ...
-
-Depends: dotur
-Homepage: http://www.plantpath.wisc.edu/fac/joh/DOTUR/
-License: GPL
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dotur/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dotur/trunk/
-Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: Defining Operational Taxonomic Units and estimating species Richness
- Dotur (Distance Based OTU and Richness determination) is a computer
- program that takes a distance matrix describing the genetic distance
- between DNA sequence data and assigns sequences to operational
- taxonomic units (OTUs) using either the furthest, average, or nearest
- neighbor algorithms for all possible distances that can be described
- using the distance matrix.  Using the OTU composition data, dotur
- constructs collector's and rarefaction curves for sampling intensity,
- richness estimators, and diversity indices.
-Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
- However, the former official homepage of this project
- http://schloss.micro.umass.edu/software/dotur.html says explicitely:
- "Please use mothur instead, feel free to contact Pat Schloss for more information."
 
 Depends: estferret
 Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
@@ -3028,6 +2989,25 @@
 X-Remark: The profnet homepage contains an image of a complete Debian system.  The Debian Med
           team tries to support the authors by providing binary packages inside Debian.
 
+Depends: abyss
+Published-Title: ABySS: A parallel assembler for short read sequence data
+Published-Authors: Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I
+Published-In: Genome Research
+Published-Year: 2009
+
+Depends: ampliconnoise
+Published-Authors: Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh
+Published-Title: Removing Noise From Pyrosequenced Amplicons
+Published-In: BMC Bioinformatics
+Published-Year: 2001
+Published-DOI: 12:38doi:10.1186/1471-2105-12-38
+
+Depends: disulfinder
+
+Suggests: circos
+
+Depends: populations
+
 Depends: denoiser
 WNPP: 587274
 Homepage:  http://www.microbio.me/denoiser/
@@ -3246,22 +3226,6 @@
 Suggests: maude
 WNPP: 611927
 
-Depends: ampliconnoise
-Homepage: http://code.google.com/p/ampliconnoise/
-License: LGPL
-Pkg-Description: Programs for the removal of noise from 454 sequenced PCR amplicons
- AmpliconNoise is a collection of programs for the removal of noise from 454
- sequenced PCR amplicons. It involves two denoising steps, the removal of noise
- from the sequencing itself and the removal of PCR point errors.
- This project also includes the Perseus algorithm for chimera removal.
-Published-Authors: Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh
-Published-Title: Removing Noise From Pyrosequenced Amplicons
-Published-In: BMC Bioinformatics
-Published-Year: 2001
-Published-DOI: 12:38doi:10.1186/1471-2105-12-38
-Remark: High relevance for NGS
-#WNPP: 624362 #The package has arrived.
-
 Depends: forge
 Homepage: http://combiol.org/forge/
 License: Apache 2.0
@@ -3712,21 +3676,6 @@
  For a full feature list you might like to visit
  http://code.google.com/p/rdkit/wiki/FeatureOverview
 
-Depends: abyss
-Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
-WNPP: 631534
-Responsible: Shaun Jackman <sjackman at debian.org>
-License: free for academic use
-Pkg-Description: a de novo, parallel, paired-end sequence assembler
- ABySS is a de novo, parallel, paired-end sequence assembler that is
- designed for short reads. It may be used to assemble genome or
- transcriptome sequence data.  Parallelization is achieved using MPI,
- OpenMP and pthread.
-Published-Title: ABySS: A parallel assembler for short read sequence data
-Published-Authors: Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I
-Published-In: Genome Research
-Published-Year: 2009
-
 Depends: python-orange
 License: GPLv3
 Homepage: http://orange.biolab.si/
@@ -3737,17 +3686,6 @@
  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.
-
-Suggests: circos
-Language: Perl
-Homepage: http://circos.ca/
-WNPP: 632174
-Responsible: Olivier Sallou <olivier.sallou at irisa.fr>
-License: GPL2+
-Pkg-Description: visualizing data in circular layout
- Circos is a software package for visualizing data and information. It
- visualizes data in a circular layout -- this makes Circos ideal for
- exploring relationships between objects or positions.
 
 Depends: raccoon
 Homepage: http://autodock.scripps.edu/resources/raccoon
@@ -3793,26 +3731,6 @@
  the confidence region for the location of a putative QTL.
  .
  The reaper module is used underneath the http://genenetwork.org site.
-
-Depends: disulfinder
-WNPP: 634177
-Homepage: http://disulfind.dsi.unifi.it/
-License: GPL2+
-Pkg-Description: prediction of S-S bonds in proteins
- 'disulfinder' is for predicting the disulfide bonding state of cysteines
- and their disulfide connectivity starting from sequence alone. Disulfide
- bridges play a major role in the stabilization of the folding process for
- several proteins. Prediction of disulfide bridges from sequence alone is
- therefore useful for the study of structural and functional properties
- of specific proteins. In addition, knowledge about the disulfide bonding
- state of cysteines may help the experimental structure determination
- process and may be useful in other genomic annotation tasks.
- .
- 'disulfinder' predicts disulfide patterns in two computational stages:
- (1) the disulfide bonding state of each cysteine is predicted by a
- BRNN-SVM binary classifier; (2) cysteines that are known to participate
- in the formation of bridges are paired by a Recursive Neural Network
- to obtain a connectivity pattern.
 
 Depends: anfo
 Homepage: http://bioinf.eva.mpg.de/anfo/

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=2961&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-phylogeny (original)
+++ projects/med/trunk/debian-med/tasks/bio-phylogeny Sun Oct  2 06:01:36 2011
@@ -305,6 +305,8 @@
 Depends: mrbayes
 
 Depends: figtree
+
+Depends: populations
 
 Depends: jstreeview
 Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml

More information about the Blends-commit mailing list