Debian Bug report logs - #669917
RFP: soap2 -- SOAPaligner of short next generation sequencing data

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

Reported by: Steffen Moeller <steffen_moeller@gmx.de>

Date: Sat, 21 Apr 2012 21:57:01 UTC

Severity: wishlist

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Report forwarded to debian-bugs-dist@lists.debian.org, debian-devel@lists.debian.org, wnpp@debian.org:
Bug#669917; Package wnpp. (Sat, 21 Apr 2012 21:57:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to Steffen Moeller <steffen_moeller@gmx.de>:
New Bug report received and forwarded. Copy sent to debian-devel@lists.debian.org, wnpp@debian.org. (Sat, 21 Apr 2012 21:57:04 GMT) Full text and rfc822 format available.

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

From: Steffen Moeller <steffen_moeller@gmx.de>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: ITP: soap2 -- SOAPaligner of short next generation sequencing data
Date: Sat, 21 Apr 2012 23:55:39 +0200
Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <steffen_moeller@gmx.de>

* Package name    : soap2
  Version         : 2.20
* URL             : http://soap.genomics.org.cn/soapaligner.html
* License         : GPL-3
  Programming Lang: C
  Description     : SOAPaligner of short next generation sequencing data

Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/soap/soap2/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soap2/

Description: <insert up to 60 chars description>
 SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis
 Package (SOAP) and an updated version of SOAP software for short
 oligonucleotide alignment (soap v1). The new program features in super
 fast and accurate alignment for huge amounts of short reads generated by
 Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order
 of magnitude faster. It require only 2 minutes aligning one million
 single-end reads onto the human reference genome. Another remarkable
 improvement of SOAPaligner is that it now supports a wide range of the
 read length.
 .
 SOAPaligner/soap2 benefitted in time and space efficiency by a revolution
 in the basic data structures and algorithms used. The core algorithms and
 the indexing data structures (2way-BWT) are developed by the algorithms
 research group of the Department of Computer Science, the University
 of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).




Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Steffen Moeller <steffen_moeller@gmx.de>:
Bug#669917; Package wnpp. (Sun, 22 Apr 2012 03:33:03 GMT) Full text and rfc822 format available.

Acknowledgement sent to Thomas Goirand <zigo@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Steffen Moeller <steffen_moeller@gmx.de>. (Sun, 22 Apr 2012 03:33:03 GMT) Full text and rfc822 format available.

Message #10 received at 669917@bugs.debian.org (full text, mbox):

From: Thomas Goirand <zigo@debian.org>
To: Steffen Moeller <steffen_moeller@gmx.de>, 669917@bugs.debian.org
Subject: Re: Bug#669917: ITP: soap2 -- SOAPaligner of short next generation sequencing data
Date: Sun, 22 Apr 2012 11:31:05 +0800
On 04/22/2012 05:55 AM, Steffen Moeller wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Steffen Moeller <steffen_moeller@gmx.de>
>
> * Package name    : soap2
>   Version         : 2.20
> * URL             : http://soap.genomics.org.cn/soapaligner.html
> * License         : GPL-3
>   Programming Lang: C
>   Description     : SOAPaligner of short next generation sequencing data
>
> Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/soap/soap2/
> Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soap2/
>
> Description: <insert up to 60 chars description>
>  SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis
>  Package (SOAP)
IMO, the package name is badly chosen. 99.99% of all Debian users
will believe that this is something concerning the SOAP network
protocol "Simple Object Access Protocol".

Would you mind to rename your package "soapaligner"?

Cheers,

Thomas





Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Steffen Moeller <steffen_moeller@gmx.de>:
Bug#669917; Package wnpp. (Sun, 22 Apr 2012 17:06:18 GMT) Full text and rfc822 format available.

Acknowledgement sent to "Steffen Möller" <steffen_moeller@gmx.de>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Steffen Moeller <steffen_moeller@gmx.de>. (Sun, 22 Apr 2012 17:06:18 GMT) Full text and rfc822 format available.

Message #15 received at 669917@bugs.debian.org (full text, mbox):

From: "Steffen Möller" <steffen_moeller@gmx.de>
To: 669917@bugs.debian.org
Subject: Re: Bug#669917: ITP: soap2 -- SOAPaligner of short next generation sequencing data
Date: Sun, 22 Apr 2012 19:05:20 +0200
Hi Thomas,
-------- Original-Nachricht --------
[...]
> > Description: <insert up to 60 chars description>
> >  SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis
> >  Package (SOAP)
> IMO, the package name is badly chosen. 99.99% of all Debian users
> will believe that this is something concerning the SOAP network
> protocol "Simple Object Access Protocol".
> 
> Would you mind to rename your package "soapaligner"?

Charge me up to those 99.99%, please. It always confuses me, too, particularly so since I was once helping the ever-ophaned gsoap package. I am less concerned about the package than with the binary, though.

There is SOAP 1,2 and 3 (with GPUs). Only v2 is called soapaligner from what I grasped.  genomics.cn-soap2 would be sufficiently distinctive and non-disrupting, I think. In the bio world that tool is fairly well known. Fine with you?

Steffen




Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Steffen Moeller <steffen_moeller@gmx.de>:
Bug#669917; Package wnpp. (Mon, 27 May 2013 14:22:00 GMT) Full text and rfc822 format available.

Acknowledgement sent to Lucas Nussbaum <lucas@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Steffen Moeller <steffen_moeller@gmx.de>. (Mon, 27 May 2013 14:22:00 GMT) Full text and rfc822 format available.

Message #20 received at 669917@bugs.debian.org (full text, mbox):

From: Lucas Nussbaum <lucas@debian.org>
To: 669917@bugs.debian.org
Cc: control@bugs.debian.org
Subject: soap2: changing back from ITP to RFP
Date: Mon, 27 May 2013 15:24:19 +0200
retitle 669917 RFP: soap2 -- SOAPaligner of short next generation sequencing data
noowner 669917
tag 669917 - pending
thanks

Hi,

This is an automatic email to change the status of soap2 back from ITP
(Intent to Package) to RFP (Request for Package), because this bug hasn't seen
any activity during the last 12 months.

If you are still interested in adopting soap2, please send a mail to
<control@bugs.debian.org> with:

 retitle 669917 ITP: soap2 -- SOAPaligner of short next generation sequencing data
 owner 669917 !
 thanks

However, it is not recommended to keep ITP for a long time without acting on
the package, as it might cause other prospective maintainers to refrain from
packaging that software. It is also a good idea to document your progress on
this ITP from time to time, by mailing <669917@bugs.debian.org>.

Thank you for your interest in Debian,
-- 
Lucas, for the QA team <debian-qa@lists.debian.org>



Changed Bug title to 'RFP: soap2 -- SOAPaligner of short next generation sequencing data' from 'ITP: soap2 -- SOAPaligner of short next generation sequencing data' Request was from Lucas Nussbaum <lucas@debian.org> to control@bugs.debian.org. (Mon, 27 May 2013 14:37:45 GMT) Full text and rfc822 format available.

Removed annotation that Bug was owned by Steffen Moeller <steffen_moeller@gmx.de>. Request was from Lucas Nussbaum <lucas@debian.org> to control@bugs.debian.org. (Mon, 27 May 2013 14:37:46 GMT) Full text and rfc822 format available.

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