--- Begin Message ---
- To: Debian Bug Tracking System <submit@bugs.debian.org>
- Subject: ITP: gbrowse -- The Generic Genome Browser from GMOD
- From: Charles Plessy <charles-debian-nospam@plessy.org>
- Date: Tue, 19 Jun 2007 12:23:40 +0900
- Message-id: <20070619032340.8947.61203.reportbug@localhost.localdomain>
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)
--- End Message ---
--- Begin Message ---
Source: gbrowse
Source-Version: 2.26~dfsg-1
We believe that the bug you reported is fixed in the latest version of
gbrowse, which is due to be installed in the Debian FTP archive:
gbrowse-calign_2.26~dfsg-1_amd64.deb
to main/g/gbrowse/gbrowse-calign_2.26~dfsg-1_amd64.deb
gbrowse-data_2.26~dfsg-1_all.deb
to main/g/gbrowse/gbrowse-data_2.26~dfsg-1_all.deb
gbrowse_2.26~dfsg-1.debian.tar.gz
to main/g/gbrowse/gbrowse_2.26~dfsg-1.debian.tar.gz
gbrowse_2.26~dfsg-1.dsc
to main/g/gbrowse/gbrowse_2.26~dfsg-1.dsc
gbrowse_2.26~dfsg-1_all.deb
to main/g/gbrowse/gbrowse_2.26~dfsg-1_all.deb
gbrowse_2.26~dfsg.orig.tar.bz2
to main/g/gbrowse/gbrowse_2.26~dfsg.orig.tar.bz2
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 429610@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <plessy@debian.org> (supplier of updated gbrowse package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 13 Apr 2011 14:45:45 +0900
Source: gbrowse
Binary: gbrowse gbrowse-data gbrowse-calign
Architecture: source all amd64
Version: 2.26~dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
gbrowse - The GMOD Generic Genome Browser
gbrowse-calign - CAlign helper
gbrowse-data - Sample data to use GBrowse
Closes: 429610
Changes:
gbrowse (2.26~dfsg-1) experimental; urgency=low
.
[ Olivier Sallou ]
* Initial Release (Closes: #429610).
Checksums-Sha1:
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5deb8d6d8891e50d8aa36214c324d9bc3a6beb81 10286481 gbrowse_2.26~dfsg.orig.tar.bz2
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96db8e2d7f8002d8ee6ea3a165801c45e62a8939 32738 gbrowse-calign_2.26~dfsg-1_amd64.deb
Checksums-Sha256:
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Files:
8b1e2766b85b114c83166768877325f1 2446 science optional gbrowse_2.26~dfsg-1.dsc
fa47761fba42f1e7315ae2fc18a75c37 10286481 science optional gbrowse_2.26~dfsg.orig.tar.bz2
d46d398dd788ba3c6b62550181da7d0b 16535 science optional gbrowse_2.26~dfsg-1.debian.tar.gz
44bd0b039730909b0577a1b6dfbe4db7 2659462 science optional gbrowse_2.26~dfsg-1_all.deb
357151d308c0bd6ad02ca10b325863f3 7555524 science optional gbrowse-data_2.26~dfsg-1_all.deb
2e6618d75f6290ea317f5a29f4f88226 32738 science optional gbrowse-calign_2.26~dfsg-1_amd64.deb
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