[Blends-commit] r3402 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Thu Jun  7 13:31:38 2012
New Revision: 3402

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3402
Log:
Remove another chunk of redundant information which is also in VCS

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=3402&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Thu Jun  7 13:31:38 2012
@@ -235,25 +235,6 @@
 Depends: dssp
 
 Depends: jellyfish
-
-Depends: meme
-Homepage: http://meme.nbcr.net/meme/
-Responsible: Steffen Moeller <moeller at debian.org>
-License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/meme/trunk/
-Pkg-Description: motif discovery and search
- MEME is a tool for discovering motifs in a group of related DNA or protein
- sequences.  A motif is a sequence pattern that occurs repeatedly in a group
- of related protein or DNA sequences. MEME represents motifs as position-dependent
- letter-probability matrices which describe the probability of each possible
- letter at each position in the pattern. Individual MEME motifs do not contain
- gaps. Patterns with variable-length gaps are split by MEME into two or more
- separate motifs.
- .
- MEME takes as input a group of DNA or protein sequences (the training set)
- and outputs as many motifs as requested. MEME uses statistical modeling
- techniques to automatically choose the best width, number of occurrences,
- and description for each motif.
 
 Depends: cytoscape
 Homepage: http://cytoscape.org/
@@ -365,9 +346,18 @@
 
 Depends: mage2tab
 
+Depends: meme
+License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
+
+Depends: microbiomeutil
+Note: In Vcs there are four binary packages however, the descriptions
+ are broken and can not be used here - this needs to be fixed first
+
 Depends: molekel
 
 Depends: mugsy
+
+Depends: murasaki
 
 Depends: ngila
 
@@ -379,7 +369,6 @@
 Language: Java
 
 Depends: pcma
-Enhances: t-coffee
 Remark: Precondition for T-Coffee
  see http://wiki.debian.org/DebianMed/TCoffee
  .
@@ -1083,25 +1072,6 @@
  integrated with the AMOS package (see http://amos.sourceforge.net/)
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: murasaki
-Homepage: http://murasaki.dna.bio.keio.ac.jp/
-License: GPL
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/murasaki/trunk/
-Pkg-Description: homology detection tool across multiple large genomes
- Murasaki is a scalable and fast, language theory-based homology
- detection tool across multiple large genomes. It enable whole-genome
- scale multiple genome global alignments. Supports unlimited length
- gapped-seed patterns and unique TF-IDF based filtering.
- .
- Murasaki is an anchor alignment software, which is
-  * exteremely fast (17 CPU hours for whole Human x Mouse genome (with
-    40 nodes: 52 wall minutes))
-  * scalable (Arbitrarily parallelizable across multiple nodes using MPI.
-    Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
-  * unlimited pattern length
-  * repeat tolerant
-  * intelligent noise reduction
-
 Depends: gmv
 Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
 License: GPL
@@ -2449,20 +2419,6 @@
  This package was requested by William Spooner <whs at eaglegenomics.com> as
  a competitor to MIRA2 and wgs-assembler.
 
-Depends: microbiomeutil
-Homepage: http://microbiomeutil.sourceforge.net/
-License: free
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/microbiomeutil/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/microbiomeutil/trunk/
-Pkg-Description: Microbiome Analysis Utilities
- The microbiomeutil package comes with the following utilities:
-  * ChimeraSlayer:  ChimeraSlayer for chimera detection.
-  * NAST-iEr:       NAST-based alignment tool.
-  * WigeoN:         A reimplementation of the Pintail 16S anomaly
-                    detection utility
-  * RESOURCES:      Reference 16S sequences and NAST-alignments that
-                    the tools above leverage.
-
 Depends: soapdenovo
 Homepage: http://soap.genomics.org.cn/soapdenovo.html
 License: GPL-3