[Blends-commit] r3395 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Wed Jun  6 13:51:36 2012
New Revision: 3395

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3395
Log:
Removed extra information from patman and prank

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=3395&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed Jun  6 13:51:36 2012
@@ -384,6 +384,8 @@
 
 Depends: pal2nal
 
+Depends: patman
+
 Depends: patristic
 Language: Java
 
@@ -396,6 +398,11 @@
  free.  Thus a change might be possible
 
 Depends: plato
+
+Depends: prank
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+ Precondition for T-Coffee (see http://wiki.debian.org/DebianMed/TCoffee)
 
 Depends: proalign
 
@@ -1175,16 +1182,6 @@
  palindromes in entire genomes very efficiently.
 Note: Download site (temporarily) not available - try to contact author
 
-Depends: patman
-Homepage: http://bioinf.eva.mpg.de/patman/
-License: GPL-2+
-WNPP: 482555
-Responsible: Charles Plessy <plessy at debian.org>
-Pkg-Description: rapid alignment of short sequences to large databases
- Patman searches for short patterns in large DNA databases, allowing
- for approximate matches. It is optimized for searching for many small
- pattern at the same time, for example microarray probes.
-
 Depends: uniprime
 Homepage: http://code.google.com/p/uniprime/
 License: GPL-3+
@@ -1972,42 +1969,6 @@
  PROSITE.
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 
-Depends: prank
-Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
-License: GPL (except two algorithms)
-Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
-Enhances: t-coffee
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
- PRANK is a probabilistic multiple alignment program for DNA, codon
- and amino-acid sequences. It's based on a novel algorithm that treats
- insertions correctly and avoids over-estimation of the number of
- deletion events. In addition, PRANK borrows ideas from maximum
- likelihood methods used in phylogenetics and correctly takes into
- account the evolutionary distances between sequences. Lastly, PRANK
- allows for defining a potential structure for sequences to be aligned
- and then, simultaneously with the alignment, predicts the locations
- of structural units in the sequences.
- .
- PRANK is a command-line program for Unix-style environments but the
- same sequence alignment engine is implemented in the graphical
- program PRANKSTER. In addition to providing a user-friendly interface
- to those not familiar with Unix systems, PRANKSTER is an alignment
- browser for alignments saved in the HSAML format. The novel format
- allows for storing all the information generated by the aligner and
- the alignment browser is a convenient way to analyse and manipulate
- the data.
- .
- PRANK aims at an evolutionarily correct sequence alignment and often
- the result looks different from ones generated with other alignment
- methods. There are, however, cases where the different look is caused
- by violations of the method's assumptions. To understand why things
- may go wrong and how to avoid that, read this explanation of
- differences between PRANK and traditional progressive alignment
- methods.
-Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
- Precondition for T-Coffee (see http://wiki.debian.org/DebianMed/TCoffee)
-
 Comment: priam
  BioLinux contains a priam package which is available at
  http://bioinfo.genotoul.fr/priam/REL_JUL06/index_jul06.html but this