Re: Role of SHOGUN in Debian Med
Hi Soeren, On Thu, Jan 24, 2013 at 10:39:54PM +0100, Soeren Sonnenburg wrote: > the issue with shogun & debian currently is that it requires ~3.5GB of > memory to compile for some of its interfaces. Build bots where choking > on this so I have no idea what to do about it. That is the reason I gave > up getting a current version into wheezy. So it is not a good idea to > more forcefully depend on this package currently. There is no thing in Blends metapackages like "forcefully Depends". In metapackages only Recommends are used and only in the case that a package is available in testing. That's technically verified at metapackage creation time. So if there are good reasons to have some package not in the current testing (as you mentioned) it will never be recommended by the metapackage but rather suggested. Regarding the suggests on the other hand we go far beyond the official package pool of Debian and we do suggest packages in non-free or even not (yet) existent in Debian. On one hand this makes sense to not always need to update the metapackages if a package we are working on enters the Debian mirror and the metapackage can also be used in derivatives with additional packages. So the relevant question whether a package should be mentioned in a certain task is always: Is a package relevant in the workfield of the task? Yes-> Recommends May be -> Suggests No -> Not mentioned in the tasks file > IMHO the most useful is the python_modular interface but surely it > depends on which language one is used to / wants to use. I don't > recommend to use any of the static interfaces nowadays (very limited > feature subset / functionality). Considering the explanation above would you agree that it makes sense to put a Suggests: shogun-python-modular into bio-dev which means even if the package would be available in testing the "Suggests" remains as a slight hint to the user that this package might be interesting even if it is not installed without forcing installation of suggests? IMHO similar questions should be asked for the Debian Science tasks[1] if you seem some task where some binray shogun package might fit here. Finally you are doing some good work in developing the software and distributing it via Debian. You should advertise this work to your potential users and the Blends approach is one way to do so. I just stumbled upon the package by pure chance even if I'm checking the Debian package pool very thorough all the time. > It certainly is one of the more popular ML toolkits. Back in academia I > did a couple of tools with it that might still be state-of-the-art, like > asp (a splice site detector) and arts (a human tss detector). Sorry, just for the sake of interest: What is a tss detector? BTW, this reminds me: It might not harm if you would try to enhance the long description of the Shogun packages a bit to enable users who are not that deeply involved into this field to draw some better conclusions. Kind regards Andreas. > On Wed, 2013-01-23 at 14:32 +0100, Andreas Tille wrote: > > > > I'm also not sure whether we should apply a stronger relation > > (=Recommends) or if SHOGUN is rather scratching a borderline field in > > bioinformatics and thus should be rather only suggested. Please be > > so kind and visit > > > > http://debian-med.alioth.debian.org/tasks/bio-dev and > > http://debian-med.alioth.debian.org/tasks/bio > > > > to see what is currently listed there to give a reasonable > > recommendation. Sorry if my question sounds a bit naive but we try to > > assemble all packages relevant for bioinformatics and sometimes the > > needed knowledge to draw a proper decision needs to be gathered > > carefully. [1] http://blends.alioth.debian.org/science/tasks/ -- 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/20130125101700.gb27...@an3as.eu
Re: Re: Flexbar source code?
Hi Andreas, Tony asked me to join discussion on Flexbar packaging. I'm not sure if the stable SeqAn 1.3.1 package release misses functionality that I rely on, or if the behaviour of functions changed even if it compiles with this release. For example the new ArgumentParser has been added rather recently and I would not be surprised if its functionality changed in the time between the SeqAn package release and the revision that I incorporated. However, I think the question is not only if it compiles somehow using this package. It should be exacly the same behaviour for one version of Flexbar. This isn't clear if the seqan sources differ in version, not to talk about slight modifications I made. Thank you for the interest to include Flexbar! Best regards Johannes -- 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/dbd338be-b4f1-4c7b-896c-c3032d981...@users.sourceforge.net
[FIS-GTM] Packing V6.0-001 - Status Update
I'm writing this mail so that interested parties know where this work stands. I had a call today (2013/01/25) with Luis Ibanez and Brad King from Kitware to get up to speed on the packaging for GT.M (thanks!). * I have an account and uploaded an SSH-key so that I can checkout and commit (thanks to Luis) * Brad helped me out with a problem applying patches based off the prior GT.M release (thanks again) * I updated the changelog to reflect the latest GT.M version, V6.0-001. * (TODO) I am using the new patch set with the V6.0-001 sources * (TODO) I will convert the get-orig-source target to pull the sources from SourceForge I will keep everyone apprised of my progress. thanks, Amul _ The information contained in this message is proprietary and/or confidential. If you are not the intended recipient, please: (i) delete the message and all copies; (ii) do not disclose, distribute or use the message in any manner; and (iii) notify the sender immediately. In addition, please be aware that any message addressed to our domain is subject to archiving and review by persons other than the intended recipient. Thank you.
Re: Flexbar source code?
Hi Johannes, many thanks for getting involved. On Fri, Jan 25, 2013 at 03:11:23PM +0100, Johannes Röhr wrote: > Tony asked me to join discussion on Flexbar packaging. I'm not sure if the > stable SeqAn 1.3.1 package release misses functionality that I rely on, or if > the behaviour of functions changed even if it compiles with this release. For > example the new ArgumentParser has been added rather recently and I would not > be surprised if its functionality changed in the time between the SeqAn > package release and the revision that I incorporated. > > However, I think the question is not only if it compiles somehow using this > package. It should be exacly the same behaviour for one version of Flexbar. > This isn't clear if the seqan sources differ in version, not to talk about > slight modifications I made. Thanks for the clarifications. I'd take this for some veto to not use the Debian packaged seqan library. The question is whether the modifications you made might be incorporated into upstream seqan. If this would be feasible we could package a seqan version that would fit flexbar (and most probably other applications.) Do you think this is possible? > Thank you for the interest to include Flexbar! Sure. We try to fit the needs of all bioinformatics tasks. Kind regards and thanks again for joining here Andreas. -- 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/20130125220803.gb12...@an3as.eu
Re: [FIS-GTM] Packing V6.0-001 - Status Update
Hi Amul, On Fri, Jan 25, 2013 at 02:45:11PM -0500, Amul Shah wrote: > I'm writing this mail so that interested parties know where this work stands. > > I had a call today (2013/01/25) with Luis Ibanez and Brad King from Kitware > to get up to speed on the packaging for GT.M (thanks!). > > * I have an account and uploaded an SSH-key so that I can checkout and > commit (thanks to Luis) > * Brad helped me out with a problem applying patches based off the prior > GT.M release (thanks again) > * I updated the changelog to reflect the latest GT.M version, V6.0-001. > * (TODO) I am using the new patch set with the V6.0-001 sources > * (TODO) I will convert the get-orig-source target to pull the sources from > SourceForge > > I will keep everyone apprised of my progress. That's really great news! I hope Luis did not forget that we try to support your attempt as best as we can - so just ask here in case of any trouble. Kind regards Andreas. -- 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/20130125221429.gc12...@an3as.eu
Re: [FIS-GTM] Packing V6.0-001 - Status Update
On Fri, Jan 25, 2013 at 5:14 PM, Andreas Tille wrote: > That's really great news! I hope Luis did not forget that we try to > support your attempt as best as we can. > Definitely have not forgotten all the help... :-) ...and how useful the MoM program was to make this possible. Cheers, Luis
