[med-svn] r10998 - in trunk/packages: . amos amos/trunk amos/trunk/debian
Andreas Tille
tille at alioth.debian.org
Thu May 24 21:26:20 UTC 2012
Author: tille
Date: 2012-05-24 21:26:20 +0000 (Thu, 24 May 2012)
New Revision: 10998
Added:
trunk/packages/amos/
trunk/packages/amos/trunk/
trunk/packages/amos/trunk/debian/
trunk/packages/amos/trunk/debian/changelog
trunk/packages/amos/trunk/debian/compat
trunk/packages/amos/trunk/debian/control
trunk/packages/amos/trunk/debian/copyright
trunk/packages/amos/trunk/debian/upstream
trunk/packages/amos/trunk/debian/watch
Log:
Add machine-readable data for amos-assembler and hawkeye which both build from the same source
Added: trunk/packages/amos/trunk/debian/changelog
===================================================================
--- trunk/packages/amos/trunk/debian/changelog (rev 0)
+++ trunk/packages/amos/trunk/debian/changelog 2012-05-24 21:26:20 UTC (rev 10998)
@@ -0,0 +1,5 @@
+amos (3.1.0-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 May 2012 14:30:13 +0200
Added: trunk/packages/amos/trunk/debian/compat
===================================================================
--- trunk/packages/amos/trunk/debian/compat (rev 0)
+++ trunk/packages/amos/trunk/debian/compat 2012-05-24 21:26:20 UTC (rev 10998)
@@ -0,0 +1 @@
+9
Added: trunk/packages/amos/trunk/debian/control
===================================================================
--- trunk/packages/amos/trunk/debian/control (rev 0)
+++ trunk/packages/amos/trunk/debian/control 2012-05-24 21:26:20 UTC (rev 10998)
@@ -0,0 +1,55 @@
+Source: amos
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://amos.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amos/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/amos/trunk/
+
+Package: amos-assembler
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+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.
+
+Package: hawkeye
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+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.
Added: trunk/packages/amos/trunk/debian/copyright
===================================================================
--- trunk/packages/amos/trunk/debian/copyright (rev 0)
+++ trunk/packages/amos/trunk/debian/copyright 2012-05-24 21:26:20 UTC (rev 10998)
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: AMOS
+Source: http://sourceforge.net/projects/amos/files/amos/
+
+Files: *
+Copyright: © 2002-2011 AMOS consortium
+License: Artistic
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: Artistic
Added: trunk/packages/amos/trunk/debian/upstream
===================================================================
--- trunk/packages/amos/trunk/debian/upstream (rev 0)
+++ trunk/packages/amos/trunk/debian/upstream 2012-05-24 21:26:20 UTC (rev 10998)
@@ -0,0 +1,32 @@
+Reference:
+ - Author: Michael C. Schatz and Adam M. Phillippy and Daniel D. Sommer and Arthur L. Delcher and Daniela Puiu and Giuseppe Narzisi and Steven L. Salzberg and Mihai Pop
+ Title: "Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies"
+ Journal: Briefings in Bioinform
+ Year: 2011
+ DOI: 10.1093/bib/bbr074
+ PMID: 22199379
+ URL: http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074
+ eprint: http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074.full.pdf+html
+ - Debian-Package: hawkeye
+ Author: Michael C Schatz and Adam M Phillippy and Ben Shneiderman and Steven L Salzberg
+ Title: "Hawkeye: an interactive visual analytics tool for genome assemblies"
+ Journal: Genome Biology
+ Year: 2007
+ Volume: 8
+ Number: 3
+ Pages: R34
+ DOI: 10.1186/gb-2007-8-3-r34
+ PMID: 17349036
+ URL: http://genomebiology.com/2007/8/3/R34
+ eprint: http://genomebiology.com/content/pdf/gb-2007-8-3-r34.pdf
+ - Debian-Package: amos-assembler
+ Author: Todd J Treangen and Dan D Sommer and Florent E Angly and Sergey Koren and Mihai Pop
+ Title: Next generation sequence assembly with AMOS
+ Journal: Curr Protoc Bioinformatics.
+ Year: 2011
+ Volume: Chapter 11
+ Pages: Unit 11.8
+ DOI: 10.1002/0471250953.bi1108s33
+ PMID: 21400694
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1108s33/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1108s33/pdf
Added: trunk/packages/amos/trunk/debian/watch
===================================================================
--- trunk/packages/amos/trunk/debian/watch (rev 0)
+++ trunk/packages/amos/trunk/debian/watch 2012-05-24 21:26:20 UTC (rev 10998)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/amos/amos-([.\d]+)\.tar\.gz
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