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Bug#429610: marked as done (ITP: gbrowse -- The Generic Genome Browser from GMOD)

Your message dated Tue, 24 Jun 2008 11:59:37 -0600
with message-id <E1KBCnp-0001cp-BV@merkel.debian.org>
and subject line WNPP bug closing
has caused the Debian Bug report #429610,
regarding ITP: gbrowse -- The Generic Genome Browser from GMOD
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
429610: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=429610
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
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 --- 
Hello,

This is an automatic mail sent to close the ITP you have reported or 
are involved with.

Your ITP wnpp bug is being closed because of the following reasons:
- It is, as of today, older than 365 days.
- It hasn't had any activity recently.

As this is an automatic procedure, it could of course have something
wrong and probably it would be closing some bugs that are not 
intended by owners and submitters (like you) to be closed, for
example if the ITP is still of your interest, or there has been 
some kind of activity around it. In that case, please reopen the
bug, do it, DO IT NOW! (I don't want to be blamed because of
mass closing and not let people know that they can easily reopen
their bugs ;-).

To re-open it, you simply have to mail control@bugs.debian.org
with a body text like this:

 reopen 429610
 stop

Further comments on the work done in the bug sent to
429610@bugs.debian.org would be truly welcomed.
Anyway, if you have any kind of problems when dealing with
the BTS, feel free to contact me and I'd be more than happy to help
you on this: <damog@debian.org>.

A similar process is being applied to other kind of wnpp bugs.

Thanks for your cooperation,

 -- David Moreno Garza <damog@debian.org>.

--- End Message ---
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