Debian Bug report logs - #710324
ITP: staden -- set of DNA sequence assembly, editing and analysis tools

Package: wnpp; Maintainer for wnpp is wnpp@debian.org;

Reported by: Jonas Smedegaard <dr@jones.dk>

Date: Wed, 29 May 2013 23:06:01 UTC

Owned by: Jonas Smedegaard <dr@jones.dk>

Severity: wishlist

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Report forwarded to debian-bugs-dist@lists.debian.org, debian-devel@lists.debian.org, wnpp@debian.org:
Bug#710324; Package wnpp. (Wed, 29 May 2013 23:06:06 GMT) Full text and rfc822 format available.

Acknowledgement sent to Jonas Smedegaard <dr@jones.dk>:
New Bug report received and forwarded. Copy sent to debian-devel@lists.debian.org, wnpp@debian.org. (Wed, 29 May 2013 23:06:06 GMT) Full text and rfc822 format available.

Message #5 received at submit@bugs.debian.org (full text, mbox):

From: Jonas Smedegaard <dr@jones.dk>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: ITP: staden -- set of DNA sequence assembly, editing and analysis tools
Date: Thu, 30 May 2013 01:02:14 +0200
Package: wnpp
Severity: wishlist
Owner: Jonas Smedegaard <dr@jones.dk>

* Package name    : staden
  Version         : 2.0.0b9
  Upstream Author : Medical Research Council, Laboratory of Molecular Biology
* URL             : http://staden.sourceforge.net/
* License         : unknown (need to be resolved, obviously, before releasing)
  Programming Lang: C, C++, Tcl
  Description     : set of DNA sequence assembly, editing and analysis tools

 This is the Staden package, a collection of sequence handling and
 analysis software.
 .
 Gap4 performs sequence assembly, contig ordering based on read pair
 data, contig joining based on sequence comparisons, assembly checking,
 repeat searching, experiment suggestion, read pair analysis and contig
 editing. It has graphical views of contigs, templates, readings and
 traces which all scroll in register. Contig editor searches and
 experiment suggestion routines use confidence values to calculate the
 confidence of the consensus sequence and hence identify only places
 requiring visual trace inspection or extra data. The result is
 extremely rapid finishing and a consensus of known accuracy.
 .
 Pregap4 provides a graphical user interface to set up the processing
 required to prepare trace data for assembly or analysis, and automates
 these processes.
 .
 Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
 ZTR trace files.
 .
 Prefinish analyses partially completed sequence assemblies and suggests
 the most efficient set of experiments to help finish the project.
 .
 Tracediff and hetscan automatically locate mutations by comparing trace
 data against reference traces. They annotate the mutations found ready
 for viewing in gap4.
 .
 Spin analyses nucleotide sequences to find genes, restriction sites,
 motifs, etc. It can perform translations, find open reading frames,
 count codons, etc. Many results are presented graphically and a sliding
 sequence window is linked to the graphics cursor. Spin also compares
 pairs of sequences in many ways. It has very rapid dot matrix analysis,
 global and local alignment algorithms, plus a sliding sequence window
 linked to the graphical plots. It can compare nucleic acid against
 nucleic acid, protein against protein, and protein against nucleic
 acid.



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Jonas Smedegaard <dr@jones.dk>:
Bug#710324; Package wnpp. (Thu, 30 May 2013 21:36:26 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@fam-tille.de>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Jonas Smedegaard <dr@jones.dk>. (Thu, 30 May 2013 21:36:26 GMT) Full text and rfc822 format available.

Message #10 received at 710324@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@fam-tille.de>
To: Jonas Smedegaard <dr@jones.dk>, 710324@bugs.debian.org
Subject: Re: Bug#710324: ITP: staden -- set of DNA sequence assembly, editing and analysis tools
Date: Thu, 30 May 2013 23:21:36 +0200
Hi Jonas,

considering you have files some bugs against staden-io-lib (version
1.12.x) you are most probably aware that we just have this:

$ apt-cache showsrc staden-io-lib
Package: staden-io-lib
Binary: staden-io-lib-utils, libstaden-read-dev, libstaden-read1
Version: 1.12.4-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>
Homepage: http://staden.sourceforge.net/
Priority: source
Section: science


In case there might be reasons to stick to the current 1.x series and it
makes sense to package 2.x in addition instead of simply upgrading I
would welcome if you would choose the Debian Med repository for doing so
(any DD has commit permissions) and set Debian Med team as maintainer.

Kind regards

        Andreas.

On Thu, May 30, 2013 at 01:02:14AM +0200, Jonas Smedegaard wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Jonas Smedegaard <dr@jones.dk>
> 
> * Package name    : staden
>   Version         : 2.0.0b9
>   Upstream Author : Medical Research Council, Laboratory of Molecular Biology
> * URL             : http://staden.sourceforge.net/
> * License         : unknown (need to be resolved, obviously, before releasing)
>   Programming Lang: C, C++, Tcl
>   Description     : set of DNA sequence assembly, editing and analysis tools
> 
>  This is the Staden package, a collection of sequence handling and
>  analysis software.
>  .
>  Gap4 performs sequence assembly, contig ordering based on read pair
>  data, contig joining based on sequence comparisons, assembly checking,
>  repeat searching, experiment suggestion, read pair analysis and contig
>  editing. It has graphical views of contigs, templates, readings and
>  traces which all scroll in register. Contig editor searches and
>  experiment suggestion routines use confidence values to calculate the
>  confidence of the consensus sequence and hence identify only places
>  requiring visual trace inspection or extra data. The result is
>  extremely rapid finishing and a consensus of known accuracy.
>  .
>  Pregap4 provides a graphical user interface to set up the processing
>  required to prepare trace data for assembly or analysis, and automates
>  these processes.
>  .
>  Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
>  ZTR trace files.
>  .
>  Prefinish analyses partially completed sequence assemblies and suggests
>  the most efficient set of experiments to help finish the project.
>  .
>  Tracediff and hetscan automatically locate mutations by comparing trace
>  data against reference traces. They annotate the mutations found ready
>  for viewing in gap4.
>  .
>  Spin analyses nucleotide sequences to find genes, restriction sites,
>  motifs, etc. It can perform translations, find open reading frames,
>  count codons, etc. Many results are presented graphically and a sliding
>  sequence window is linked to the graphics cursor. Spin also compares
>  pairs of sequences in many ways. It has very rapid dot matrix analysis,
>  global and local alignment algorithms, plus a sliding sequence window
>  linked to the graphical plots. It can compare nucleic acid against
>  nucleic acid, protein against protein, and protein against nucleic
>  acid.
> 
> 
> -- 
> To UNSUBSCRIBE, email to debian-devel-REQUEST@lists.debian.org
> with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
> Archive: http://lists.debian.org/20130529230214.27412.61045.reportbug@auryn.jones.dk
> 
> 

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Jonas Smedegaard <dr@jones.dk>:
Bug#710324; Package wnpp. (Fri, 31 May 2013 01:03:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to 710324@bugs.debian.org:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Jonas Smedegaard <dr@jones.dk>. (Fri, 31 May 2013 01:03:04 GMT) Full text and rfc822 format available.

Message #15 received at 710324@bugs.debian.org (full text, mbox):

From: Jonas Smedegaard <dr@jones.dk>
To: Andreas Tille <andreas@fam-tille.de>, 710324@bugs.debian.org
Subject: Re: Bug#710324: ITP: staden -- set of DNA sequence assembly, editing and analysis tools
Date: Fri, 31 May 2013 03:01:21 +0200
[Message part 1 (text/plain, inline)]
Quoting Andreas Tille (2013-05-30 23:21:36)
> considering you have files some bugs against staden-io-lib (version 
> 1.12.x) you are most probably aware that we just have this:
> 
> $ apt-cache showsrc staden-io-lib
[snip]
> In case there might be reasons to stick to the current 1.x series and 
> it makes sense to package 2.x in addition instead of simply upgrading 
> I would welcome if you would choose the Debian Med repository for 
> doing so (any DD has commit permissions) and set Debian Med team as 
> maintainer.

staden and staden-io-lib are not the same thing. In fact, staden (some 
applications) depends on staden-io-lib (library implementing read-write 
routines for some file formats) - which explains why I bumped into some 
issues with the libraries leading to bugreports ;-)

Nevertheless, if the Debian Med team has a low-volume mailinglist and 
don't mind my use of CDBS for packaging, I will be happy to have staden 
be part of that team.


 - Jonas

-- 
 * Jonas Smedegaard - idealist & Internet-arkitekt
 * Tlf.: +45 40843136  Website: http://dr.jones.dk/

 [x] quote me freely  [ ] ask before reusing  [ ] keep private
[signature.asc (application/pgp-signature, inline)]

Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Jonas Smedegaard <dr@jones.dk>:
Bug#710324; Package wnpp. (Fri, 31 May 2013 05:51:17 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@fam-tille.de>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Jonas Smedegaard <dr@jones.dk>. (Fri, 31 May 2013 05:51:17 GMT) Full text and rfc822 format available.

Message #20 received at 710324@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@fam-tille.de>
To: 710324@bugs.debian.org
Subject: Re: Bug#710324: ITP: staden -- set of DNA sequence assembly, editing and analysis tools
Date: Fri, 31 May 2013 07:49:09 +0200
Hi Jonas,

On Fri, May 31, 2013 at 03:01:21AM +0200, Jonas Smedegaard wrote:
> > In case there might be reasons to stick to the current 1.x series and 
> > it makes sense to package 2.x in addition instead of simply upgrading 
> > I would welcome if you would choose the Debian Med repository for 
> > doing so (any DD has commit permissions) and set Debian Med team as 
> > maintainer.
> 
> staden and staden-io-lib are not the same thing. In fact, staden (some 
> applications) depends on staden-io-lib (library implementing read-write 
> routines for some file formats) - which explains why I bumped into some 
> issues with the libraries leading to bugreports ;-)

Ahh, I should have checked this before sending this mail.

> Nevertheless, if the Debian Med team has a low-volume mailinglist and 

I have no idea what might be your limit for low-volume - there are some
mails per day thought.  If you are only interested in this specific
package you might consider just subscribing this package via PTS as
alternative.

> don't mind my use of CDBS for packaging,

I admit I tend to convert from cdbs to dh but we have several packages
left with cdbs.  Finally we are not that kind of people who would try to
convert the cdbs maintainer to something else. ;-)

> I will be happy to have staden 
> be part of that team.

This would be really cool.

Kind regards

      Andreas.

-- 
http://fam-tille.de



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