Bug#429610: ITP: gbrowse -- The Generic Genome Browser from GMOD
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>
Package name : gbrowse
Version : 1.68
Upstream Author : Lincoln Stein & the GMOD team (gmod-gbrowse@lists.sourceforge.net)
URL : http://www.gmod.org/wiki/index.php/GBrowse
License : Same as Perl, plus additional clauses (see below)
Programming Lang: Perl
Description : The Generic Genome Browser from GMOD
The Generic Genome Browser is a combination of database and interactive Web
page for manipulating and displaying annotations on genomes. Some of its
features:
* Simultaneous bird's eye and detailed views of the genome.
* Scroll, zoom, center.
* Attach arbitrary URLs to any annotation.
* Order and appearance of tracks are customizable by administrator and end-user.
* Search by annotation ID, name, or comment.
* Supports third party annotation using GFF formats.
* Settings persist across sessions.
* DNA and GFF dumps.
* Connectivity to different databases, including BioSQL and Chado.
* Multi-language support.
* Third-party feature loading.
* Customizable plug-in architecture (e.g. run BLAST, dump & import many formats,
find oligonucleotides, design primers, create restriction maps, edit features)
.
Homepage: http://www.gmod.org/wiki/index.php/GBrowse
I have made a draft package for my own use at work and uploaded it in
Debian-Med's SVN. (http://svn.debian.org/wsvn/debian-med/trunk/packages/gbrowse)
Gbrowse needs bioperl 1.5.2 which is not yet available in Debian (work in
progress...) Moreover, I have a few older ITPs to finish first. But if you are
interested in Gbrowse, please contact me in private: I can change my
priorities.
Full DISCLAIMER file:
---------------------------------
The Generic Genome Browser package and all associated files are
Copyright (c) 2002 Cold Spring Harbor Laboratory and University of
California, Berkeley.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See the Artistic License file
in the main Perl distribution for specific terms and conditions of
use. In addition, the following disclaimers apply:
CSHL makes no representations whatsoever as to the SOFTWARE contained
herein. It is experimental in nature and is provided WITHOUT WARRANTY
OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER
WARRANTY, EXPRESS OR IMPLIED. CSHL MAKES NO REPRESENTATION OR
WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR
OTHER PROPRIETARY RIGHT.
By downloading this SOFTWARE, your Institution hereby indemnifies CSHL
against any loss, claim, damage or liability, of whatsoever kind or
nature, which may arise from your Institution's respective use,
handling or storage of the SOFTWARE.
If publications result from research using this SOFTWARE, we ask that
CSHL and University of California, Berkeley be acknowledged and/or
credit be given to CSHL/Berkeley scientists, as scientifically
appropriate.
-------------------------
Unfortunately, the indemnification clause makes gbrowse incompatible with the
GPL. Is it possible to recursively explore the dependancy graph of gbrowse to
check that there is no GPL-only program in in ? In the long term, maybe Debtags
could be useful for this...
-- Charles Plessy
-- System Information:
Debian Release: 4.0
APT prefers stable
APT policy: (500, 'stable')
Architecture: i386 (i686)
Shell: /bin/sh linked to /bin/dash
Kernel: Linux 2.6.18-4-486
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
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