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 <[email protected]> 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 <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
