[Blends-commit] r2792 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Fri Apr 29 06:40:11 2011
New Revision: 2792

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2792
Log:
Seq-gen and transtermhp now official 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=2792&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Apr 29 06:40:11 2011
@@ -180,6 +180,8 @@
  of them.
 
 Depends: mothur, bowtie
+
+Depends: transtermhp
 
 X-End-Category: Sequence alignments and related programs.
 
@@ -355,6 +357,8 @@
 Remark: Do not upgrade this package
  Steffen Möller is scientifically collaborating with upstream and nothing shall
  happen to that package until authors give their confirmation.
+
+Depends: seq-gen
 
 Depends: bagphenotype
 Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
@@ -1045,24 +1049,6 @@
  .
  Probably it makes sense to remove this project from the prospective packages
  list.
-
-Depends: seq-gen
-Homepage: http://tree.bio.ed.ac.uk/software/seqgen/
-License: GPL-3.0
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seq-gen/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seq-gen/trunk/
-Pkg-Description: simulate the evolution of nucleotide or amino acid sequences
- Seq-Gen is a program that will simulate the evolution of nucleotide or
- amino acid sequences along a phylogeny, using common models of the
- substitution process. A range of models of molecular evolution are
- implemented including the general reversible model. State frequencies
- and other parameters of the model may be given and site-specific rate
- heterogeneity may also be incorporated in a number of ways. Any number
- of trees may be read in and the program will produce any number of data
- sets for each tree. Thus large sets of replicate simulations can be easily
- created. It has been designed to be a general purpose simulator that
- incorporates most of the commonly used (and computationally tractable)
- models of molecular sequence evolution.
 
 Depends: wgs-assembler
 Homepage: http://wgs-assembler.sourceforge.net/
@@ -1682,21 +1668,6 @@
  A software tool was implemented that computes exact repeats and
  palindromes in entire genomes very efficiently.
 Note: Download site (temporarily) not available - try to contact author
-
-Depends: transtermhp
-Homepage: http://transterm.cbcb.umd.edu/index.php
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tm-align/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/tm-align/trunk/
-License: GPL 2+
-Pkg-Description: finds rho-independent transcription terminators in bacterial genomes
- finds rho-independent transcription terminators in bacterial
- genomes. Each terminator found by the program is assigned a
- confidence value that estimates its probability of being a true
- terminator. TransTermHP is described in: C. Kingsford, K. Ayanbule
- and S.L. Salzberg. Rapid, accurate, computational discovery of
- Rho-independent transcription terminators illuminates their
- relationship to DNA uptake. Genome Biology 8:R22 (2007).
-Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
 
 Depends: patman
 Homepage: http://bioinf.eva.mpg.de/patman/
@@ -3880,4 +3851,4 @@
 	 http://www.eve.ucdavis.edu/rcthomson/phylis/
 Comment: SEQanswers: The next generation sequencing community
 	 http://seqanswers.com/forums/showthread.php?t=43
-
+Comment: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)