[Blends-commit] r3145 - /projects/med/trunk/debian-med/tasks/bio

Sat Feb 18 18:00:37 UTC 2012

Author: tille
Date: Sat Feb 18 18:00:37 2012
New Revision: 3145

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3145
Log:
Removed extra information for three packages; added "References_in_debian_upstream: yes" for cufflinks

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=3145&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sat Feb 18 18:00:37 2012
@@ -519,6 +519,19 @@
 Depends: raxml
 
 Depends: mlv-smile
+
+Suggests: cain
+
+Depends: cd-hit
+
+Depends: cufflinks
+X-References_in_debian_upstream: yes
+Published-Authors: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
+Published-Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
+Published-In: Nature Biotechnology
+Published-DOI: doi:10.1038/nbt.1621
+Published-URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
+Published-Year: 2010
 
 Depends: axparafit
 Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
@@ -2107,36 +2120,6 @@
  cap3 and formcon, dated Aug 29, 2002.  This package exists purely for
  convenience to Bio-Linux users so that the files are placed in
  locations consistent with the Bio-Linux setup.
-
-Depends: cd-hit
-Homepage: http://www.bioinformatics.org/cd-hit/
-License: GPLv2
-WNPP: 652074
-Responsible: Andreas Tille <tille at debian.org>
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cd-hit/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cd-hit/trunk/
-Pkg-Description: suite of programs designed to quickly group sequences.
- CD-HIT stands for Cluster Database at High Identity with
- Tolerance. The program (cd-hit) takes a fasta format sequence
- database as input and produces a set of 'non-redundant' (nr)
- representative sequences as output. In addition cd-hit outputs a
- cluster file, documenting the sequence 'groupies' for each nr
- sequence representative. The idea is to reduce the overall size of
- the database without removing any sequence information by only
- removing 'redundant' (or highly similar) sequences. This is why the
- resulting database is called non-redundant (nr). Essentially, cd-hit
- produces a set of closely related protein families from a given fasta
- sequence database.
- .
- CD-HIT uses a 'longest sequence first' list removal algorithm to
- remove sequences above a certain identity threshold. Additionally the
- algorithm implements a very fast heuristic to find high identity
- segments between sequences, and so can avoid many costly full
- alignments.
- .
- With recent developments, cd-hit package offers new programs for DNA
- sequence clustering and comparing two databases. It also has lots of
- new options for clustering control.
 
 Comment: BioLinux contains a clcworkbench package which is available
  at http://www.clcbio.com/index.php?id=28 but this seems to be only
@@ -2975,26 +2958,6 @@
 Published-URL: http://genomebiology.com/2009/10/11/R134
 Published-DOI: 10.1186/gb-2009-10-11-r134
 
-Depends: cufflinks
-WNPP: 627799
-Homepage: http://cufflinks.cbcb.umd.edu/
-Vcs-Git: git://git.debian.org/debian-med/cufflinks.git
-Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary
-License: Boost
-X-Category: Sequencing
-Pkg-Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq
- Cufflinks assembles transcripts, estimates their abundances, and tests for
- differential expression and regulation in RNA-Seq samples. It accepts aligned
- RNA-Seq reads and assembles the alignments into a parsimonious set of
- transcripts. Cufflinks then estimates the relative abundances of these
- transcripts based on how many reads support each one.
-Published-Authors: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
-Published-Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-Published-In: Nature Biotechnology
-Published-DOI: doi:10.1038/nbt.1621
-Published-URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
-Published-Year: 2010
-
 Depends: ncbi-blast+
 
 Depends: treetime
@@ -3776,31 +3739,6 @@
  detect true associations. The EIGENSOFT package has a built-in plotting
  script and supports multiple file formats and quantitative phenotypes.
 
-Suggests: cain
-License: BSD like
-Homepage: http://cain.sourceforge.net
-Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/cain/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cain/trunk/
-Pkg-Description: simulations of chemical reactions
- Cain performs stochastic and deterministic simulations of chemical reactions.
- It can spawn multiple simulation processes to utilize multi-core computers.
- It stores models, methods, and simulation output (populations and reaction
- counts) in an XML format. In addition, SBML models can be imported and
- exported. The models and methods can be read from input files or edited
- within the program.
- .
- The GUI (Graphical User Interface) is written in Python and uses the wxPython
- toolkit. Most of the solvers are implemented as command line executables,
- written in C++, which are driven by Cain. This makes it easy to launch batch
- jobs. It also simplifies the process of adding new solvers. Cain offers a
- variety of solvers:
-  * Gillespie's direct method.
-  * Gillespie's first reaction method.
-  * Gibson and Bruck's next reaction method.
-  * Tau-leaping.
-  * Hybrid direct/tau-leaping.
-  * ODE integration.
-
 Depends: sequenceconverter.app
 Homepage: http://bioinformatics.org/biococoa/
 License: GPL


