[Blends-commit] r3360 - /projects/med/trunk/debian-med/tasks/bio

Thu May 24 21:28:19 UTC 2012

Author: tille
Date: Thu May 24 21:28:19 2012
New Revision: 3360

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3360
Log:
Remove extra information from amos-assembler and hawkeye which are now in SVN

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=3360&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Thu May 24 21:28:19 2012
@@ -322,6 +322,9 @@
 X-Mark: Packages in Vcs - Information about these is queried from UDD as well
 
 Depends: agdbnet
+
+Depends: amos-assembler, hawkeye
+Language: Perl
 
 Depends: anfo
 
@@ -1031,25 +1034,6 @@
  3.5-fold in total application time when aligning reads from recent
  sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
  technologies.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-
-Depends: amos-assembler
-Homepage: http://amos.sourceforge.net/
-License: Artistic
-Language: Perl
-X-Category: Genome assembling
-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.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
 Depends: amoscmp
@@ -1198,39 +1182,6 @@
  .
  Note that currently Bambus is undergoing a transition in order to be
  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: hawkeye
-Homepage: http://amos.sourceforge.net/hawkeye/
-License: Artistic
-Pkg-Description: Interactive Visual Analytics Tool for Genome Assemblies
- Genome assembly remains an inexact science. Even when accomplished
- with the best software available, the assembly of a genome often
- contains numerous errors, both small and large. Hawkeye is a visual
- analytics tool for genome assembly analysis and validation, designed
- to aid in identifying and correcting assembly errors. Hawkeye blends
- the best practices from information and scientific visualization to
- facilitate inspection of large-scale assembly data while minimizing
- the time needed to detect mis-assemblies and make accurate judgments
- of assembly quality.
- .
- All levels of the assembly data hierarchy are made accessible to
- users, along with summary statistics and common assembly metrics. A
- ranking component guides investigation towards likely mis-assemblies
- or interesting features to support the task at hand. Wherever
- possible, high-level overviews, dynamic filtering, and automated
- clustering are leveraged to focus attention and highlight anomalies
- in the data. Hawkeyes effectiveness has been proven on several genome
- projects, where it has been used both to improve quality and to
- validate the correctness of complex genomes.
- .
- Hawkeye is compatible with most widely used assemblers, including
- Phrap, ARACHNE, Celera Assembler, Newbler, AMOS, and assemblies
- deposited in the NCBI Assembly Archive.
- .
- Publication: Schatz, M.C., Phillippy, A.M., Shneiderman, B.,
- Salzberg, S.L. (2007) Hawkeye: a visual analytics tool for genome
- assemblies. Genome Biology 8:R34.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
 Depends: murasaki


