[Cdd-commits] r1072 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Tue Sep  9 07:27:55 2008
New Revision: 1072

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added lucy


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Sep  9 07:27:55 2008
@@ -2134,25 +2134,6 @@
  BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
  a package.
 
-Depends: lamarc
-Homepage: http://evolution.gs.washington.edu/lamarc/
-License: Apache V2.0
-Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: estimate population-genetic parameters
- LAMARC is a program which estimates population-genetic parameters
- such as population size, population growth rate, recombination rate,
- and migration rates. It approximates a summation over all possible
- genealogies that could explain the observed sample, which may be
- sequence, SNP, microsatellite, or electrophoretic data. LAMARC and
- its sister program Migrate are successor programs to the older
- programs Coalesce, Fluctuate, and Recombine, which are no longer
- being supported. The programs are memory-intensive but can run
- effectively on workstations.
- .
- This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
-
 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 ...
@@ -2406,3 +2387,50 @@
  .
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Depends: lamarc
+Homepage: http://evolution.gs.washington.edu/lamarc/
+License: Apache V2.0
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: estimate population-genetic parameters
+ LAMARC is a program which estimates population-genetic parameters
+ such as population size, population growth rate, recombination rate,
+ and migration rates. It approximates a summation over all possible
+ genealogies that could explain the observed sample, which may be
+ sequence, SNP, microsatellite, or electrophoretic data. LAMARC and
+ its sister program Migrate are successor programs to the older
+ programs Coalesce, Fluctuate, and Recombine, which are no longer
+ being supported. The programs are memory-intensive but can run
+ effectively on workstations.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: lucy
+Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
+License: GPL
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: DNA sequence quality and vector trimming tool
+ Lucy is a utility that prepares raw DNA sequence fragments for
+ sequence assembly, possibly using the TIGR Assembler. The cleanup
+ process includes quality assessment, confidence reassurance, vector
+ trimming and vector removal. The primary advantage of Lucy over other
+ similar utilities is that it is a fully integrated, stand alone
+ program.
+ .
+ Lucy was designed and written at The Institute for Genomic Research
+ (TIGR, now the J. Craig Venter Institute), and it has been used here
+ for several years to clean sequence data from automated DNA
+ sequencers prior to sequence assembly and other downstream uses.  The
+ quality trimming portion of lucy makes use of phred quality scores,
+ such as those produced by many automated sequencers based on the
+ Sanger sequencing method.  As such, lucy’s quality trimming may not
+ be appropriate for sequence data produced by some of the new
+ “next-generation” sequencers.
+ .
+ See also the SourceForge page at http://lucy.sourceforge.net/.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html