[Cdd-commits] r700 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Thu Apr 10 08:23:54 2008
New Revision: 700

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added amos and smile; while smile has a note that even if packaging stuff exists
this seems to be not really worth to turn it into an official package.


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Thu Apr 10 08:23:54 2008
@@ -1074,7 +1074,7 @@
  GlimmerHMM.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
 
-Depends: riso
+Ignore: riso
 Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
 License: not specified
 Pkg-Description: motif discovery tool
@@ -1097,6 +1097,32 @@
  The reference to SMILE is made here especially because there is some
  work done in the Debian Med SVN at
  http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/?rev=0&sc=0
+ .
+ On the other hand the SMILE author told us in private mail that he
+ thinks that RISO is dead and SMILE continues to have some importance.
+
+Ignore: smile
+Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
+License: GPL
+WNPP: 221492
+Responsible: Steffen Moeller <moeller at debian.org>
+Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/?rev=0&sc=0
+Pkg-Description: Find statistically significant patterns in sequences
+ Smile determines sequence motifs on the basis of a set of DNA, RNA or
+ protein sequences. The work was originally described in the Journal of
+ Computational Biology (2000) 7:345-362 and has since been developed
+ further.
+  * No hard limit on the number of combinations of motifs to describe
+    subsets of sequences.
+  * The sequence alphabet may be specified.
+  * The use of wildcards is supported.
+  * Better determination of significance of motifs by simulation.
+  * Introduction of a set of sequences with negative controls
+    that should not match automatically determined motifs.
+ .
+ Note: We do not know anybody who actually uses SMILE and thus the
+ packaging effort is stalled.  Feel free to tell us, if you are
+ interested in turning this into an official package.
 
 Depends: mummergpu
 Homepage: http://mummergpu.sourceforge.net/
@@ -1124,3 +1150,19 @@
  3.5-fold in total application time when aligning reads from recent
  sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
  technologies.
+
+Depends: amos-assembler
+Homepage: http://amos.sourceforge.net/
+License: Artistic
+Pkg-Description: modular whole genome assembler
+ The AMOS consortium is committed to the development of open-source
+ whole genome assembly software. The project acronym (AMOS) represents
+ our primary goal -- to produce A Modular, Open-Source whole genome
+ assembler. Open-source so that everyone is welcome to contribute and
+ help build outstanding assembly tools, and modular in nature so that
+ new contributions can be easily inserted into an existing assembly
+ pipeline. This modular design will foster the development of new
+ assembly algorithms and allow the AMOS project to continually grow
+ and improve in hopes of eventually becoming a widely accepted and
+ deployed assembly infrastructure. In this sense, AMOS is both a
+ design philosophy and a software system.