[Blends-commit] r3034 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Fri Nov  4 08:49:11 2011
New Revision: 3034

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3034
Log:
jellyfish now in unstable

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=3034&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Nov  4 08:49:11 2011
@@ -431,6 +431,13 @@
 Depends: squizz
 
 Depends: clonalframe
+
+Depends: jellyfish
+Published-Title: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
+Published-Authors: Guillaume Marcais and Carl Kingsford
+Published-In: Bioinformatics
+Published-Year: 2011
+Published-DOI: 10.1093/bioinformatics/btr011
 
 Depends: r-other-genabel
 Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
@@ -3788,31 +3795,6 @@
   * Hybrid direct/tau-leaping.
   * ODE integration.
 
-Depends: jellyfish
-License: GPL-3+
-Homepage: http://www.cbcb.umd.edu/software/jellyfish/
-WNPP: 644925
-Responsible: Shaun Jackman <sjackman at gmail.com>
-Pkg-Description: count k-mers of DNA
- JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
- DNA. A k-mer is a substring of length k, and counting the occurrences
- of all such substrings is a central step in many analyses of DNA
- sequence. JELLYFISH can count k-mers using an order of magnitude less
- memory and an order of magnitude faster than other k-mer counting
- packages by using an efficient encoding of a hash table and by
- exploiting the "compare-and-swap" CPU instruction to increase
- parallelism.
- .
- JELLYFISH is a command-line program that reads FASTA and multi-FASTA
- files containing DNA sequences. It outputs its k-mer counts in an
- binary format, which can be translated into a human-readable text
- format using the "jellyfish dump" command.
-Published-Title: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-Published-Authors: Guillaume Marcais and Carl Kingsford
-Published-In: Bioinformatics
-Published-Year: 2011
-Published-DOI: 10.1093/bioinformatics/btr011
-
 Depends: sequenceconverter.app
 Homepage: http://bioinformatics.org/biococoa/
 License: GPL