Debian Bug report logs - #724280
ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene

version graph

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

Reported by: Simon Kainz <simon@familiekainz.at>

Date: Mon, 23 Sep 2013 10:00:01 UTC

Owned by: Simon Kainz <simon@familiekainz.at>

Severity: wishlist

Fixed in versions rtax/0.984-1, rtax/0.984-2

Done: Charles Plessy <plessy@debian.org>

Bug is archived. No further changes may be made.

Toggle useless messages

View this report as an mbox folder, status mbox, maintainer mbox


Report forwarded to debian-bugs-dist@lists.debian.org, debian-devel@lists.debian.org, wnpp@debian.org:
Bug#724280; Package wnpp. (Mon, 23 Sep 2013 10:00:05 GMT) Full text and rfc822 format available.

Acknowledgement sent to Simon Kainz <simon@familiekainz.at>:
New Bug report received and forwarded. Copy sent to debian-devel@lists.debian.org, wnpp@debian.org. (Mon, 23 Sep 2013 10:00:05 GMT) Full text and rfc822 format available.

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

From: Simon Kainz <simon@familiekainz.at>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Mon, 23 Sep 2013 11:56:03 +0200
Package: wnpp
Severity: wishlist
Owner: Simon Kainz <simon@familiekainz.at>

* Package name    : rtax
  Version         :  0.983
  Upstream Author : David A. W. Soergel <David A. W. Soergel>
* URL             : David A. W. Soergel
* License         : BSD
  Programming Lang: Perl
  Description     : Rapid and accurate taxonomic classification of short
paired-end sequence reads from the 16S ribosomal RNA gene

Short-read technologies for microbial community profiling are increasingly
popular, yet previous techniques for assigning taxonomy to paired-end reads
perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads
using a consensus algorithm.

This tool is an optional dependency for qiime(which is already packaged) and it
would be great to have it
packaged for Debian.

Regards,

Simon



Added tag(s) pending. Request was from Anibal Monsalve Salazar <anibal@debian.org> to control@bugs.debian.org. (Tue, 24 Sep 2013 20:06:14 GMT) Full text and rfc822 format available.

Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Simon Kainz <simon@familiekainz.at>:
Bug#724280; Package wnpp. (Wed, 25 Sep 2013 06:36:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to Thomas Weber <tweber@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Simon Kainz <simon@familiekainz.at>. (Wed, 25 Sep 2013 06:36:04 GMT) Full text and rfc822 format available.

Message #12 received at 724280@bugs.debian.org (full text, mbox):

From: Thomas Weber <tweber@debian.org>
To: 724280@bugs.debian.org
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Wed, 25 Sep 2013 08:32:22 +0200
Hi Simon, 

some nitpicking:

On Mon, Sep 23, 2013 at 11:56:03AM +0200, Simon Kainz wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Simon Kainz <simon@familiekainz.at>
> 
> * Package name    : rtax
>   Version         :  0.983
>   Upstream Author : David A. W. Soergel <David A. W. Soergel>
> * URL             : David A. W. Soergel
> * License         : BSD
>   Programming Lang: Perl
>   Description     : Rapid and accurate taxonomic classification of short
> paired-end sequence reads from the 16S ribosomal RNA gene

Please shorten the short description.
> 
> Short-read technologies for microbial community profiling are increasingly
> popular, yet previous techniques for assigning taxonomy to paired-end reads
> perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads
> using a consensus algorithm.

I would drop the first sentence - this sounds a lot like the first
sentence in a scientific paper.

Best,
Thomas



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org:
Bug#724280; Package wnpp. (Thu, 26 Sep 2013 21:36:08 GMT) Full text and rfc822 format available.

Acknowledgement sent to Simon Kainz <simon@familiekainz.at>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org. (Thu, 26 Sep 2013 21:36:08 GMT) Full text and rfc822 format available.

Message #17 received at 724280@bugs.debian.org (full text, mbox):

From: Simon Kainz <simon@familiekainz.at>
To: Thomas Weber <tweber@debian.org>, <724280@bugs.debian.org>
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Thu, 26 Sep 2013 23:27:51 +0200
Am 2013-09-25 08:32, schrieb Thomas Weber:
> Hi Simon,
>
> some nitpicking:
>
> On Mon, Sep 23, 2013 at 11:56:03AM +0200, Simon Kainz wrote:
>> Package: wnpp
>> Severity: wishlist
>> Owner: Simon Kainz <simon@familiekainz.at>
>>
>> * Package name    : rtax
>>   Version         :  0.983
>>   Upstream Author : David A. W. Soergel <David A. W. Soergel>
>> * URL             : David A. W. Soergel
>> * License         : BSD
>>   Programming Lang: Perl
>>   Description     : Rapid and accurate taxonomic classification of 
>> short
>> paired-end sequence reads from the 16S ribosomal RNA gene
>
> Please shorten the short description.
>>
>> Short-read technologies for microbial community profiling are 
>> increasingly
>> popular, yet previous techniques for assigning taxonomy to 
>> paired-end reads
>> perform poorly. RTAX provides rapid taxonomic assignments of 
>> paired-end reads
>> using a consensus algorithm.
>
> I would drop the first sentence - this sounds a lot like the first
> sentence in a scientific paper.
>
> Best,
> Thomas


Hi!

Thank you for you suggestions.

Well, i already uploaded (actually, my sponsor) the package to the NEW 
queue. Currently it is sitting there. Now I'm unsure as to make the 
changes you suggested, and quickly reupload or just wait to get the 
package uploaded and then, after it is not "new" to Debian anymore, 
upload the fixed version. Any suggestions? I just want to minimize the 
work for the FTP-Masters caused by my new package.

Regards,

Simon



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Simon Kainz <simon@familiekainz.at>:
Bug#724280; Package wnpp. (Sat, 28 Sep 2013 19:57:08 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@an3as.eu>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Simon Kainz <simon@familiekainz.at>. (Sat, 28 Sep 2013 19:57:08 GMT) Full text and rfc822 format available.

Message #22 received at 724280@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@an3as.eu>
To: Simon Kainz <simon@familiekainz.at>, 724280@bugs.debian.org
Cc: Debian Med Project List <debian-med@lists.debian.org>
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Sat, 28 Sep 2013 21:51:57 +0200
Hi Simon,

this package is a perfect target for Debian Med but I noticed you are
not yet a member of the Alioth team.  Since I'm currently on vaccation
and not frequently online I just added skainz-guest to the Debian Med
team simply assuming you might consider using Debian Med VCS as
described in our team policy[1].  I hope you agree with this and please
let us know if you need any help with the packaging.

Kind regards

       Andreas.

[1] http://debian-med.alioth.debian.org/docs/policy.html

On Mon, Sep 23, 2013 at 11:56:03AM +0200, Simon Kainz wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Simon Kainz <simon@familiekainz.at>
> 
> * Package name    : rtax
>   Version         :  0.983
>   Upstream Author : David A. W. Soergel <David A. W. Soergel>
> * URL             : David A. W. Soergel
> * License         : BSD
>   Programming Lang: Perl
>   Description     : Rapid and accurate taxonomic classification of short
> paired-end sequence reads from the 16S ribosomal RNA gene
> 
> Short-read technologies for microbial community profiling are increasingly
> popular, yet previous techniques for assigning taxonomy to paired-end reads
> perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads
> using a consensus algorithm.
> 
> This tool is an optional dependency for qiime(which is already packaged) and it
> would be great to have it
> packaged for Debian.
> 
> Regards,
> 
> Simon
> 
> 
> -- 
> 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/20130923095603.26061.18627.reportbug@zidpc9027.tu-graz.ac.at
> 
> 

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org:
Bug#724280; Package wnpp. (Sun, 29 Sep 2013 07:21:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to Simon Kainz <simon@familiekainz.at>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org. (Sun, 29 Sep 2013 07:21:04 GMT) Full text and rfc822 format available.

Message #27 received at 724280@bugs.debian.org (full text, mbox):

From: Simon Kainz <simon@familiekainz.at>
To: Andreas Tille <andreas@an3as.eu>, "724280@bugs.debian.org" <724280@bugs.debian.org>
Cc: "724280@bugs.debian.org" <724280@bugs.debian.org>, Debian Med Project List <debian-med@lists.debian.org>
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Sun, 29 Sep 2013 09:18:58 +0200
Hello!

Thank you very much. My package is already in the NEW queue, and after quickly inspecting the Debian Med Policy, i suspect i have to change some entries in the control file (at least) to make it compliant to the Debian Med Policy. So should I just reupload the package after applying my changes or should i wait for FTPMasters to either accept or reject the package. I just want to keep the work needed for the FTPMasters as small as possible, so maybe someone might give ma a hint as how to handle this. 

Concerning packaging: For packaging itself, i think i don't need help- i already did some packaging work (for some local packages used ad work) and i have a very competent sponsor which helped me to create my packages.

I will try to get my work into alioth/debian-med. I will contact debian-med when I am getting stuck, so be prepared for some questions :-)

Regards,

Simon


> Am 28.09.2013 um 21:51 schrieb Andreas Tille <andreas@an3as.eu>:
> 
> Hi Simon,
> 
> this package is a perfect target for Debian Med but I noticed you are
> not yet a member of the Alioth team.  Since I'm currently on vaccation
> and not frequently online I just added skainz-guest to the Debian Med
> team simply assuming you might consider using Debian Med VCS as
> described in our team policy[1].  I hope you agree with this and please
> let us know if you need any help with the packaging.
> 
> Kind regards
> 
>       Andreas.
> 
> [1] http://debian-med.alioth.debian.org/docs/policy.html
> 
>> On Mon, Sep 23, 2013 at 11:56:03AM +0200, Simon Kainz wrote:
>> Package: wnpp
>> Severity: wishlist
>> Owner: Simon Kainz <simon@familiekainz.at>
>> 
>> * Package name    : rtax
>>  Version         :  0.983
>>  Upstream Author : David A. W. Soergel <David A. W. Soergel>
>> * URL             : David A. W. Soergel
>> * License         : BSD
>>  Programming Lang: Perl
>>  Description     : Rapid and accurate taxonomic classification of short
>> paired-end sequence reads from the 16S ribosomal RNA gene
>> 
>> Short-read technologies for microbial community profiling are increasingly
>> popular, yet previous techniques for assigning taxonomy to paired-end reads
>> perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads
>> using a consensus algorithm.
>> 
>> This tool is an optional dependency for qiime(which is already packaged) and it
>> would be great to have it
>> packaged for Debian.
>> 
>> Regards,
>> 
>> Simon
>> 
>> 
>> -- 
>> 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/20130923095603.26061.18627.reportbug@zidpc9027.tu-graz.ac.at
> 
> -- 
> http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Simon Kainz <simon@familiekainz.at>:
Bug#724280; Package wnpp. (Sun, 29 Sep 2013 09:45:08 GMT) Full text and rfc822 format available.

Acknowledgement sent to Thomas Weber <tweber@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Simon Kainz <simon@familiekainz.at>. (Sun, 29 Sep 2013 09:45:08 GMT) Full text and rfc822 format available.

Message #32 received at 724280@bugs.debian.org (full text, mbox):

From: Thomas Weber <tweber@debian.org>
To: Simon Kainz <simon@familiekainz.at>, 724280@bugs.debian.org
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Sun, 29 Sep 2013 11:41:39 +0200
On Thu, Sep 26, 2013 at 11:27:51PM +0200, Simon Kainz wrote:
> Hi!
> 
> Thank you for you suggestions.
> 
> Well, i already uploaded (actually, my sponsor) the package to the
> NEW queue. 

No need to rush things - you can change these things later. 

	Thomas



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Simon Kainz <simon@familiekainz.at>:
Bug#724280; Package wnpp. (Sun, 29 Sep 2013 18:42:09 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@an3as.eu>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Simon Kainz <simon@familiekainz.at>. (Sun, 29 Sep 2013 18:42:09 GMT) Full text and rfc822 format available.

Message #37 received at 724280@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@an3as.eu>
To: Simon Kainz <simon@familiekainz.at>
Cc: "724280@bugs.debian.org" <724280@bugs.debian.org>, Debian Med Project List <debian-med@lists.debian.org>
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Sun, 29 Sep 2013 20:37:40 +0200
Hi Simon,

On Sun, Sep 29, 2013 at 09:18:58AM +0200, Simon Kainz wrote:
> Thank you very much. My package is already in the NEW queue,

Fine.

> and after quickly inspecting the Debian Med Policy, i suspect i have to change some entries in the control file (at least) to make it compliant to the Debian Med Policy. So should I just reupload the package after applying my changes or should i wait for FTPMasters to either accept or reject the package. I just want to keep the work needed for the FTPMasters as small as possible, so maybe someone might give ma a hint as how to handle this. 

It's perfectly OK to wait for ftpmaster response and leave the package
in new as is.  I have added rtax to the Debian Med bio task as you can
see on the according tasks page.[1]
 
> Concerning packaging: For packaging itself, i think i don't need help- i already did some packaging work (for some local packages used ad work) and i have a very competent sponsor which helped me to create my packages.

We do absolutely not want to disrupt your workflow / relation to your
sponsor.  It is just an offer since in some cases it has turned out to
be hard to find a sponsor.

> I will try to get my work into alioth/debian-med.

That would be great and hopefully helpfull also for your work.

> I will contact debian-med when I am getting stuck, so be prepared for some questions :-)

That's what we are keen on. :-)
 
Kind regards

     Andreas.

[1] http://debian-med.alioth.debian.org/tasks/bio#rtax
 
> > Am 28.09.2013 um 21:51 schrieb Andreas Tille <andreas@an3as.eu>:
> > 
> > Hi Simon,
> > 
> > this package is a perfect target for Debian Med but I noticed you are
> > not yet a member of the Alioth team.  Since I'm currently on vaccation
> > and not frequently online I just added skainz-guest to the Debian Med
> > team simply assuming you might consider using Debian Med VCS as
> > described in our team policy[1].  I hope you agree with this and please
> > let us know if you need any help with the packaging.
> > 
> > Kind regards
> > 
> >       Andreas.
> > 
> > [1] http://debian-med.alioth.debian.org/docs/policy.html
> > 
> >> On Mon, Sep 23, 2013 at 11:56:03AM +0200, Simon Kainz wrote:
> >> Package: wnpp
> >> Severity: wishlist
> >> Owner: Simon Kainz <simon@familiekainz.at>
> >> 
> >> * Package name    : rtax
> >>  Version         :  0.983
> >>  Upstream Author : David A. W. Soergel <David A. W. Soergel>
> >> * URL             : David A. W. Soergel
> >> * License         : BSD
> >>  Programming Lang: Perl
> >>  Description     : Rapid and accurate taxonomic classification of short
> >> paired-end sequence reads from the 16S ribosomal RNA gene
> >> 
> >> Short-read technologies for microbial community profiling are increasingly
> >> popular, yet previous techniques for assigning taxonomy to paired-end reads
> >> perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads
> >> using a consensus algorithm.
> >> 
> >> This tool is an optional dependency for qiime(which is already packaged) and it
> >> would be great to have it
> >> packaged for Debian.
> >> 
> >> Regards,
> >> 
> >> Simon
> >> 
> >> 
> >> -- 
> >> 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/20130923095603.26061.18627.reportbug@zidpc9027.tu-graz.ac.at
> > 
> > -- 
> > http://fam-tille.de
> 

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Simon Kainz <simon@familiekainz.at>:
Bug#724280; Package wnpp. (Thu, 21 Nov 2013 16:21:20 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@an3as.eu>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Simon Kainz <simon@familiekainz.at>. (Thu, 21 Nov 2013 16:21:20 GMT) Full text and rfc822 format available.

Message #42 received at 724280@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@an3as.eu>
To: Simon Kainz <simon@familiekainz.at>
Cc: "724280@bugs.debian.org" <724280@bugs.debian.org>, Debian Med Project List <debian-med@lists.debian.org>
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Thu, 21 Nov 2013 17:19:37 +0100
Hi Simon,

I have not seen the package in NEW any more and also I can not find a
package with this name inside the pool.  So it seems it has not passed
ftpmasters check.  Do you have some VCS with the packaging (or
preferably might like to use Debian Med VCS)?

Kind regards

       Andreas.

On Sun, Sep 29, 2013 at 08:37:40PM +0200, Andreas Tille wrote:
> Hi Simon,
> 
> On Sun, Sep 29, 2013 at 09:18:58AM +0200, Simon Kainz wrote:
> > Thank you very much. My package is already in the NEW queue,
> 
> Fine.
> 
> > and after quickly inspecting the Debian Med Policy, i suspect i have to change some entries in the control file (at least) to make it compliant to the Debian Med Policy. So should I just reupload the package after applying my changes or should i wait for FTPMasters to either accept or reject the package. I just want to keep the work needed for the FTPMasters as small as possible, so maybe someone might give ma a hint as how to handle this. 
> 
> It's perfectly OK to wait for ftpmaster response and leave the package
> in new as is.  I have added rtax to the Debian Med bio task as you can
> see on the according tasks page.[1]
>  
> > Concerning packaging: For packaging itself, i think i don't need help- i already did some packaging work (for some local packages used ad work) and i have a very competent sponsor which helped me to create my packages.
> 
> We do absolutely not want to disrupt your workflow / relation to your
> sponsor.  It is just an offer since in some cases it has turned out to
> be hard to find a sponsor.
> 
> > I will try to get my work into alioth/debian-med.
> 
> That would be great and hopefully helpfull also for your work.
> 
> > I will contact debian-med when I am getting stuck, so be prepared for some questions :-)
> 
> That's what we are keen on. :-)
>  
> Kind regards
> 
>      Andreas.
> 
> [1] http://debian-med.alioth.debian.org/tasks/bio#rtax
>  
> > > Am 28.09.2013 um 21:51 schrieb Andreas Tille <andreas@an3as.eu>:
> > > 
> > > Hi Simon,
> > > 
> > > this package is a perfect target for Debian Med but I noticed you are
> > > not yet a member of the Alioth team.  Since I'm currently on vaccation
> > > and not frequently online I just added skainz-guest to the Debian Med
> > > team simply assuming you might consider using Debian Med VCS as
> > > described in our team policy[1].  I hope you agree with this and please
> > > let us know if you need any help with the packaging.
> > > 
> > > Kind regards
> > > 
> > >       Andreas.
> > > 
> > > [1] http://debian-med.alioth.debian.org/docs/policy.html
> > > 
> > >> On Mon, Sep 23, 2013 at 11:56:03AM +0200, Simon Kainz wrote:
> > >> Package: wnpp
> > >> Severity: wishlist
> > >> Owner: Simon Kainz <simon@familiekainz.at>
> > >> 
> > >> * Package name    : rtax
> > >>  Version         :  0.983
> > >>  Upstream Author : David A. W. Soergel <David A. W. Soergel>
> > >> * URL             : David A. W. Soergel
> > >> * License         : BSD
> > >>  Programming Lang: Perl
> > >>  Description     : Rapid and accurate taxonomic classification of short
> > >> paired-end sequence reads from the 16S ribosomal RNA gene
> > >> 
> > >> Short-read technologies for microbial community profiling are increasingly
> > >> popular, yet previous techniques for assigning taxonomy to paired-end reads
> > >> perform poorly. RTAX provides rapid taxonomic assignments of paired-end reads
> > >> using a consensus algorithm.
> > >> 
> > >> This tool is an optional dependency for qiime(which is already packaged) and it
> > >> would be great to have it
> > >> packaged for Debian.
> > >> 
> > >> Regards,
> > >> 
> > >> Simon
> > >> 
> > >> 
> > >> -- 
> > >> 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/20130923095603.26061.18627.reportbug@zidpc9027.tu-graz.ac.at
> > > 
> > > -- 
> > > http://fam-tille.de
> > 
> 
> -- 
> http://fam-tille.de
> 
> 
> -- 
> To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
> with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
> Archive: http://lists.debian.org/20130929183740.GA12433@an3as.eu
> 
> 

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org:
Bug#724280; Package wnpp. (Tue, 26 Nov 2013 13:30:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to Simon Kainz <simon@familiekainz.at>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org. (Tue, 26 Nov 2013 13:30:04 GMT) Full text and rfc822 format available.

Message #47 received at 724280@bugs.debian.org (full text, mbox):

From: Simon Kainz <simon@familiekainz.at>
To: Andreas Tille <andreas@an3as.eu>
Cc: "724280@bugs.debian.org" <724280@bugs.debian.org>, Debian Med Project List <debian-med@lists.debian.org>
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Tue, 26 Nov 2013 14:16:16 +0100
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Am 2013-11-21 17:19, schrieb Andreas Tille:
> Hi Simon,
> 
> I have not seen the package in NEW any more and also I can not find
> a package with this name inside the pool.  So it seems it has not
> passed ftpmasters check.  Do you have some VCS with the packaging
> (or preferably might like to use Debian Med VCS)?
> 

Hello!

Sorry for the delay, currently i have quite a lot to do.

After studying the Debian Med Policy, i have a questions:

Should i just import the upstream source into alioth, or just my
changes (eg /debian directory + patches)?

Sorry if this seems dumb, I don't want to screw things up.

I contacted upstream und he fixed the licensing issue ( added license
text to easier-to-find places), so it will hopefully make it into the
new queue.


Thank you.

Simon




> Kind regards
> 
> Andreas.
> 
> On Sun, Sep 29, 2013 at 08:37:40PM +0200, Andreas Tille wrote:
>> Hi Simon,
>> 
>> On Sun, Sep 29, 2013 at 09:18:58AM +0200, Simon Kainz wrote:
>>> Thank you very much. My package is already in the NEW queue,
>> 
>> Fine.
>> 
>>> and after quickly inspecting the Debian Med Policy, i suspect i
>>> have to change some entries in the control file (at least) to
>>> make it compliant to the Debian Med Policy. So should I just
>>> reupload the package after applying my changes or should i wait
>>> for FTPMasters to either accept or reject the package. I just
>>> want to keep the work needed for the FTPMasters as small as
>>> possible, so maybe someone might give ma a hint as how to
>>> handle this.
>> 
>> It's perfectly OK to wait for ftpmaster response and leave the
>> package in new as is.  I have added rtax to the Debian Med bio
>> task as you can see on the according tasks page.[1]
>> 
>>> Concerning packaging: For packaging itself, i think i don't
>>> need help- i already did some packaging work (for some local
>>> packages used ad work) and i have a very competent sponsor
>>> which helped me to create my packages.
>> 
>> We do absolutely not want to disrupt your workflow / relation to
>> your sponsor.  It is just an offer since in some cases it has
>> turned out to be hard to find a sponsor.
>> 
>>> I will try to get my work into alioth/debian-med.
>> 
>> That would be great and hopefully helpfull also for your work.
>> 
>>> I will contact debian-med when I am getting stuck, so be
>>> prepared for some questions :-)
>> 
>> That's what we are keen on. :-)
>> 
>> Kind regards
>> 
>> Andreas.
>> 
>> [1] http://debian-med.alioth.debian.org/tasks/bio#rtax
>> 
>>>> Am 28.09.2013 um 21:51 schrieb Andreas Tille
>>>> <andreas@an3as.eu>:
>>>> 
>>>> Hi Simon,
>>>> 
>>>> this package is a perfect target for Debian Med but I noticed
>>>> you are not yet a member of the Alioth team.  Since I'm
>>>> currently on vaccation and not frequently online I just added
>>>> skainz-guest to the Debian Med team simply assuming you might
>>>> consider using Debian Med VCS as described in our team
>>>> policy[1].  I hope you agree with this and please let us know
>>>> if you need any help with the packaging.
>>>> 
>>>> Kind regards
>>>> 
>>>> Andreas.
>>>> 
>>>> [1] http://debian-med.alioth.debian.org/docs/policy.html
>>>> 
>>>>> On Mon, Sep 23, 2013 at 11:56:03AM +0200, Simon Kainz
>>>>> wrote: Package: wnpp Severity: wishlist Owner: Simon Kainz
>>>>> <simon@familiekainz.at>
>>>>> 
>>>>> * Package name    : rtax Version         :  0.983 Upstream
>>>>> Author : David A. W. Soergel <David A. W. Soergel> * URL
>>>>> : David A. W. Soergel * License         : BSD Programming
>>>>> Lang: Perl Description     : Rapid and accurate taxonomic
>>>>> classification of short paired-end sequence reads from the
>>>>> 16S ribosomal RNA gene
>>>>> 
>>>>> Short-read technologies for microbial community profiling
>>>>> are increasingly popular, yet previous techniques for
>>>>> assigning taxonomy to paired-end reads perform poorly. RTAX
>>>>> provides rapid taxonomic assignments of paired-end reads 
>>>>> using a consensus algorithm.
>>>>> 
>>>>> This tool is an optional dependency for qiime(which is
>>>>> already packaged) and it would be great to have it packaged
>>>>> for Debian.
>>>>> 
>>>>> Regards,
>>>>> 
>>>>> Simon
>>>>> 
>>>>> 
>>>>> -- 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/20130923095603.26061.18627.reportbug@zidpc9027.tu-graz.ac.at
>>>>
>>>>
>>>>> 
- -- 
>>>> http://fam-tille.de
>>> 
>> 
>> -- http://fam-tille.de
>> 
>> 
>> -- To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org 
>> with a subject of "unsubscribe". Trouble? Contact
>> listmaster@lists.debian.org Archive:
>> http://lists.debian.org/20130929183740.GA12433@an3as.eu
>> 
>> 
> 

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
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=emWa
-----END PGP SIGNATURE-----



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Simon Kainz <simon@familiekainz.at>:
Bug#724280; Package wnpp. (Tue, 26 Nov 2013 15:15:12 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@an3as.eu>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Simon Kainz <simon@familiekainz.at>. (Tue, 26 Nov 2013 15:15:12 GMT) Full text and rfc822 format available.

Message #52 received at 724280@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@an3as.eu>
To: Simon Kainz <simon@familiekainz.at>
Cc: "724280@bugs.debian.org" <724280@bugs.debian.org>, Debian Med Project List <debian-med@lists.debian.org>
Subject: Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
Date: Tue, 26 Nov 2013 16:10:26 +0100
Hi Simon.

On Tue, Nov 26, 2013 at 02:16:16PM +0100, Simon Kainz wrote:
> Sorry for the delay, currently i have quite a lot to do.

Just take your time.
 
> After studying the Debian Med Policy, i have a questions:
> 
> Should i just import the upstream source into alioth, or just my
> changes (eg /debian directory + patches)?

This depends from the Vcs of your choice.  When using git please follow
the detailed advise to import pristine tar.  In case you prefer SVN we
just keep the debian/ dir.

> Sorry if this seems dumb, I don't want to screw things up.

Askin in advance is perfectly welcome - hope my answer is precise
enough.

> I contacted upstream und he fixed the licensing issue ( added license
> text to easier-to-find places), so it will hopefully make it into the
> new queue.

Cool.  Just let us know if you might need any further help.

Kind regards

       Andreas.

-- 
http://fam-tille.de



Reply sent to Simon Kainz <simon@familiekainz.at>:
You have taken responsibility. (Sun, 29 Dec 2013 11:03:27 GMT) Full text and rfc822 format available.

Notification sent to Simon Kainz <simon@familiekainz.at>:
Bug acknowledged by developer. (Sun, 29 Dec 2013 11:03:27 GMT) Full text and rfc822 format available.

Message #57 received at 724280-close@bugs.debian.org (full text, mbox):

From: Simon Kainz <simon@familiekainz.at>
To: 724280-close@bugs.debian.org
Subject: Bug#724280: fixed in rtax 0.984-1
Date: Sun, 29 Dec 2013 11:00:07 +0000
Source: rtax
Source-Version: 0.984-1

We believe that the bug you reported is fixed in the latest version of
rtax, which is due to be installed in the Debian FTP archive.

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 724280@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Simon Kainz <simon@familiekainz.at> (supplier of updated rtax 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@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Wed, 27 Nov 2013 09:50:23 +0100
Source: rtax
Binary: rtax
Architecture: source all
Version: 0.984-1
Distribution: unstable
Urgency: low
Maintainer: Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Simon Kainz <simon@familiekainz.at>
Description: 
 rtax       - Classification of sequence reads of 16S ribosomal RNA gene
Closes: 724280
Changes: 
 rtax (0.984-1) unstable; urgency=low
 .
   * Initial release. (Closes: #724280)
   * Removed broken magic to find scripts-subdir,
     because we know where rtax is installed (set_script_dir.path)
   * Change interpreter to bash to prevent syntax
     error warnings (fix-bash-syntax-error.patch)
   * Added minimal manpage.
Checksums-Sha1: 
 38e38ba6986e29d7d7f844cb399cb9f2e4b87284 1228 rtax_0.984-1.dsc
 823549298daa4cd95147e38eb4dea52618e92b4a 23662 rtax_0.984.orig.tar.gz
 4ad0cf9c27fd83ad341c5aaa44cb4f723d535e6b 4112 rtax_0.984-1.debian.tar.gz
 6249f77254580b74073fde3f40aaf715627cabae 25720 rtax_0.984-1_all.deb
Checksums-Sha256: 
 ed73e605f077d7ff62fa68959ad2d7e353fa6ef173ed07d00365c7c54e926bc3 1228 rtax_0.984-1.dsc
 92ad9a881ca1d17221794b4313654291b30df6a9edcd0453034a090ae13a3442 23662 rtax_0.984.orig.tar.gz
 1e18f989ba46ef0e422eed5f4d19165635b310ee1b99b0e77c74c7c8cddf6ceb 4112 rtax_0.984-1.debian.tar.gz
 20df37defaad05c4f8d8b06f01dea7cedab82999bd476bd7977e22998f124f78 25720 rtax_0.984-1_all.deb
Files: 
 2c26e9c0c02d752264c6a15602060129 1228 science optional rtax_0.984-1.dsc
 e9dbbe4b3c26b0f0f6c14a5fb46aa587 23662 science optional rtax_0.984.orig.tar.gz
 90f37c65fa5a8f563e9d10ce47fcb457 4112 science optional rtax_0.984-1.debian.tar.gz
 9e2f29067c38b7ac71e0035b993eba31 25720 science optional rtax_0.984-1_all.deb

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.15 (GNU/Linux)

iEYEARECAAYFAlKXHvEACgkQYDBbMcCf01okUACfRdfdPu7a9c6JqIpC12ZcNYgt
IRIAnistO5pmfMp3YbRdM0R3CBPR6zkr
=8Vdc
-----END PGP SIGNATURE-----




Reply sent to Charles Plessy <plessy@debian.org>:
You have taken responsibility. (Sun, 29 Dec 2013 11:03:31 GMT) Full text and rfc822 format available.

Notification sent to Simon Kainz <simon@familiekainz.at>:
Bug acknowledged by developer. (Sun, 29 Dec 2013 11:03:31 GMT) Full text and rfc822 format available.

Message #62 received at 724280-close@bugs.debian.org (full text, mbox):

From: Charles Plessy <plessy@debian.org>
To: 724280-close@bugs.debian.org
Subject: Bug#724280: fixed in rtax 0.984-2
Date: Sun, 29 Dec 2013 11:00:08 +0000
Source: rtax
Source-Version: 0.984-2

We believe that the bug you reported is fixed in the latest version of
rtax, which is due to be installed in the Debian FTP archive.

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 724280@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 rtax 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@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Sat, 28 Dec 2013 12:56:34 +0100
Source: rtax
Binary: rtax
Architecture: source all
Version: 0.984-2
Distribution: unstable
Urgency: medium
Maintainer: Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description: 
 rtax       - Classification of sequence reads of 16S ribosomal RNA gene
Closes: 724280
Changes: 
 rtax (0.984-2) unstable; urgency=medium
 .
   * Team upload.
   * Corrected the name of the copyright holders.
 .
 rtax (0.984-1) unstable; urgency=low
 .
   * Initial release. (Closes: #724280)
   * Removed broken magic to find scripts-subdir,
     because we know where rtax is installed (set_script_dir.path)
   * Change interpreter to bash to prevent syntax
     error warnings (fix-bash-syntax-error.patch)
   * Added minimal manpage.
Checksums-Sha1: 
 fb5ef114b3dbba72c90d8911c01390598dc0c391 1868 rtax_0.984-2.dsc
 823549298daa4cd95147e38eb4dea52618e92b4a 23662 rtax_0.984.orig.tar.gz
 0aa53d56650f32b85ba94ef5c73559322e14bb3b 4263 rtax_0.984-2.debian.tar.gz
 23fb1a06e9951c517d270b8b36ffa76f132efe54 25758 rtax_0.984-2_all.deb
Checksums-Sha256: 
 f0219b5dc4eecbb1d62180b711db45ba0fdbe494266b6a9159577698b8de3d47 1868 rtax_0.984-2.dsc
 92ad9a881ca1d17221794b4313654291b30df6a9edcd0453034a090ae13a3442 23662 rtax_0.984.orig.tar.gz
 9173e449dacc1f9d9b040a2cb55ab84d2e082d70d4023049a56a0462061a9ed3 4263 rtax_0.984-2.debian.tar.gz
 c8b19f4965868fe707e73042ab9c70263aac8431e8bb5771392344d46f81546d 25758 rtax_0.984-2_all.deb
Files: 
 15b024566fbddba9c7d4cb7d10955596 1868 science optional rtax_0.984-2.dsc
 e9dbbe4b3c26b0f0f6c14a5fb46aa587 23662 science optional rtax_0.984.orig.tar.gz
 98529e44c1aac32c37eb602d18bf0cee 4263 science optional rtax_0.984-2.debian.tar.gz
 51a62daa55e098186fb5e485ebdabd29 25758 science optional rtax_0.984-2_all.deb

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.15 (GNU/Linux)
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=DLcA
-----END PGP SIGNATURE-----




Bug archived. Request was from Debbugs Internal Request <owner@bugs.debian.org> to internal_control@bugs.debian.org. (Mon, 27 Jan 2014 07:35:46 GMT) Full text and rfc822 format available.

Send a report that this bug log contains spam.


Debian bug tracking system administrator <owner@bugs.debian.org>. Last modified: Sat Apr 19 07:04:47 2014; Machine Name: beach.debian.org

Debian Bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.