Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
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 : > > 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 >> >> * Package name: rtax >> Version : 0.983 >> Upstream Author : 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-requ...@lists.debian.org >> with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org >> Archive: >> http://lists.debian.org/20130923095603.26061.18627.report...@zidpc9027.tu-graz.ac.at > > -- > http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/ff05672a-b5ed-46eb-b657-bc787ef04...@familiekainz.at
Re: Biological data being used by an unpublished research paper is considered proprietary
Hi Karsten, On Wed, 25 Sep 2013 22:11:07 +0200, Karsten Hilbert wrote: > On Wed, Sep 25, 2013 at 10:37:18PM +0530, Faheem Mitha wrote: > >> It is not really a big >> deal either way, but if I had some definite information > > There is no definite information to be had because it is > exactly that: different opinion in different places. > > And that's mostly due to people being either stupid or > greedy. Or both. (Or not-yet-educated on the issue in which > case providing information so they can decide on a license > *sometimes* works.) Thank you for your replies. I only just saw them, because I am not actually subscribed to any Debian mailing lists, and either read replies if they are CCed to me, or read them via gmane (as I am doing now) possibly some time after they have been posted. I don't always remember to say "CC me please" in my posts, and people don't always CC me if I do. Still, I wish there was a way to make a permanent sticky thing for my posts to mailing lists (which 99% of the time I am not subscribed to) saying "CC me please". I guess if I was more techy than I am, I would have a setup where my signature to mailing lists included a "CC please". Anyway, from what you and others are saying there is no definite general legal answer about whether biological data can be proprietary. This is not welcome news, but is unsurprising. I hope these issues will be clarified eventually, so that biological data can universally be considered public domain or similar. If you or anyone else know of any ongoing work to clarify this issue, can you link to it? Thanks. Regards, Faheem -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/slrnl4gou9.b95.fah...@chrestomanci.home.earth
Re: getting some R packages into Debian
Hi Andreas, On Tue, 10 Sep 2013 08:57:58 +0200, Andreas Tille wrote: > Hi Faheem, > > could you please stop CCing me. I also guess you are subscribed - so I > also stop CCing you. I don't receive mail from Debian lists unless I'm CCed, so please do CC me. Hence, I didn't see your message till now. I'm reading it via gmane. I'll try to remember not to CC you. Apparently the Debian mailing list rules say that if someone wants to be CCed he/she should says so. > On Tue, Sep 10, 2013 at 02:19:29AM +0530, Faheem Mitha wrote: >> >>Question 2: >> >>http://debian-med.alioth.debian.org/docs/policy.html#repositories >> >>only talks about Subversion and Git. Given that choice, I'd >> >>definitely go with Git, but is Mercurial out as an option? >> >No. We considering two options as sufficient for everybody. Otherwise >> >the main supporters might be forced to learn more and more tools which >> >is not acceptable in the end. >> I think you meant to say "yes" to the question "is Mercurial out as >> an option?", right? :-) > Yes (you are right and to the original question) ;-) >> Looks like I'll actually have to learn Git. > The things you need for packaging are a very limited set to learn and > our policy document explains the main things you should notice. >> Crap. > IMHO it would be better if you base your emotions on facts like > "According to [Link] foo is better than bar." Simple statements of > dissatisfaction are not really healthy for mailing list communication. This was meant semi-humorously. In any case, I don't see the problem with expressions of feeling. I'm sorry if you didn't like it. Regards, Faheem -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/slrnl4gqn2.b95.fah...@chrestomanci.home.earth
Re: Bug#724280: ITP: rtax -- Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene
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 : > > > > 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 > >> > >> * Package name: rtax > >> Version : 0.983 > >> Upstream Author : 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-requ...@lists.debian.org > >> with a subject of "unsubscribe". Trouble? Contact > >> listmas...@lists.debian.org > >> Archive: > >> http://lists.debian.org/20130923095603.26061.18627.report...@zidpc9027.tu-graz.ac.at > > > > -- > > http://fam-tille.de > -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130929183740.ga12...@an3as.eu
