Re: [Soc-coordination] Possible GSoC idea: Cloud images for bioinformatics.
Le Fri, Feb 22, 2013 at 09:04:12AM +0900, Charles Plessy a écrit : > > I would like to propose a bottom-up project with the goal of setting an > infrastructure or workflow allowing one to build and use easily a Debian (Med) > image where given bioinformatics tools are available at a version selected by > the user (tapping in snapshots.debian.org or perhaps other repository within > our web of trust if necessary). Hi all, I have written a stub on the 2013's wiki page. http://wiki.debian.org/SummerOfCode2013/Projects#Project_idea:_a_cloud_image_for_bioinformatics_with_Debian Simply booting a Wheezy image and typing 'apt-get install med-cloud' definitely does not need two month of full-time work (one summer of coding), and it has already been mentionned that Cloud Bio-Linux is already distributing our packages in cloud images. I think that to be successful, proposals have to address other problems, in particular the need for precise versions of software, or the need for images that will happily crunch hundreds of gigabytes of data, or the need for parallelisation of workflows, etc. Have a nice week-end, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- 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/20130223083023.ga2...@falafel.plessy.net
Re: [Soc-coordination] Possible GSoC idea: Cloud images for bioinformatics.
Le Fri, Feb 22, 2013 at 08:24:58PM +0800, James Bromberger a écrit : > > I'm conscious of the point release 6.0.7 due real soon now - I've spoken > with Anders to tag a new point release of the ec2debian-build-ami script > which fixes a number of issues since 6.0.6 (such as deleting the root > EBS volume on Terminate in AWS). Beyond that I think we should now be > looking to target Wheezy - is that a fair target, or would people like a > Debian-med Squeeze AMI available as well? Hi James, I think that for Debian Med, Wheezy is definitely the target. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- 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/20130223083206.gb2...@falafel.plessy.net
Re: Draft version of article for Indian health care journal
Hi again, I just learned that it seems to be hard to obtain the viewable PDF from SVN and so I've putted a copy online here: http://people.debian.org/~tille/tmp-healthcafe-article/debian-med-healthcafe.pdf Sorry for the confusion Andreas. On Fri, Feb 22, 2013 at 08:59:36PM +0100, Andreas Tille wrote: > Hi, > > I added a ready build PDF and it is accessible via > > > http://anonscm.debian.org/viewvc/debian-med/trunk/community/papers/13_healthcafe/ > > as well. > > Kind regards and thanks for checking > > Andreas. > > On Fri, Feb 22, 2013 at 08:53:20PM +0100, Karsten Hilbert wrote: > > Andreas, can you please post an http accessible link for > > > > >> and so I commited a draft to SVN[2]. > > ... > > >> [2] > > >> svn://svn.debian.org/svn/debian-med/trunk/community/papers/13_healthcafe > > > > Thanks, > > Karsten > > -- > > GPG key ID E4071346 @ gpg-keyserver.de > > E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346 > > > > -- > 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/20130222195936.gb1...@an3as.eu > > -- 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/20130223092121.ga21...@an3as.eu
Re: [Soc-coordination] Possible GSoC idea: Cloud images for bioinformatics.
On Sat, Feb 23, 2013 at 05:30:23PM +0900, Charles Plessy wrote: > Simply booting a Wheezy image and typing 'apt-get install med-cloud' > definitely > does not need two month of full-time work (one summer of coding), and it has > already been mentionned that Cloud Bio-Linux is already distributing our > packages in cloud images. +1 > I think that to be successful, proposals have to address other problems, in > particular the need for precise versions of software, or the need for images > that will happily crunch hundreds of gigabytes of data, or the need for > parallelisation of workflows, etc. I agree that these things are reasonable and "not yet invented" things but I think this is missing in the project description. 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/20130223093400.gb21...@an3as.eu
Re: [Soc-coordination] Possible GSoC idea: Cloud images for bioinformatics.
Le Sat, Feb 23, 2013 at 10:34:00AM +0100, Andreas Tille a écrit : > On Sat, Feb 23, 2013 at 05:30:23PM +0900, Charles Plessy wrote: > > Simply booting a Wheezy image and typing 'apt-get install med-cloud' > > definitely > > does not need two month of full-time work (one summer of coding), and it has > > already been mentionned that Cloud Bio-Linux is already distributing our > > packages in cloud images. > > +1 > > > I think that to be successful, proposals have to address other problems, in > > particular the need for precise versions of software, or the need for images > > that will happily crunch hundreds of gigabytes of data, or the need for > > parallelisation of workflows, etc. > > I agree that these things are reasonable and "not yet invented" things > but I think this is missing in the project description. Good point: I updated the description as follows. http://wiki.debian.org/SummerOfCode2013/Projects#Project_idea:_a_cloud_image_for_bioinformatics_with_Debian Description of the project: This is a call for bottom-up proposals structured by students themselves along the following lines. 2012 has been a year of progresses in Debian's support for clouds. Combined with Debian's leadership in the distribution of packaged scientific and medical software, this opens opportunities for establishing Debian as a first-class provider of virtualised solutions for bioinformatics. To be successful, proposals will need to go beyond simply booting a Wheezy image and typing apt-get install med-cloud, and take into account the prior art of Cloud Bio-Linux, which is already distributing our packages in cloud images. They will have to address other problems, such as the need for precise versions of software, the need for images that will happily crunch hundreds of gigabytes of data, the need for parallelisation of workflows, etc. Cheers, -- Charles (By the way, I am on emboss' copyright file) -- 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/20130223094625.gc2...@falafel.plessy.net
Re: Packaging hunspell-en-med
Am 22.02.2013 23:03, schrieb Sukhbir Singh: > Hi Tobias, > > I am trying to package `hunspell-en-med', a dictionary of English > medical terms for Debian Med. I have done the packaging and it is ready > [0], but somehow the package is not working as it should be as I am > unable to use the dictionary in OpenOffice. > > Since you have packaged a similar dictionary in the past > (hunspell-de-med), maybe you could help us in pinpointing the source of > the problem? > > [0] - > http://anonscm.debian.org/gitweb/?p=debian-med/hunspell-en-med.git;a=summary > > Thanks! > > (PS: I have CCed the Debian Med mailing list but please feel free to > reply in private if you want) Hi Sukhbir Singh, unfortunately, I cannot help you, because I'm facing the exact same problem with the german variant. This is an old, long-standing bug[1] which I'm still unable to solve. Regards, Tobias [1] https://bugs.launchpad.net/medicalterms/+bug/401423 signature.asc Description: OpenPGP digital signature
Re: Packaging hunspell-en-med
Hi, interesting to know that there is such problem. The next valuable resource of knowledge in questions like this would be the Debian Mentors list - so I'd suggest to forward the problem to debian-ment...@lists.debian.org and ask for help. Probably it makes sense to forward the bug below[0] to the Debian BTS to have a proper reference. Kind regards Andreas. On Sat, Feb 23, 2013 at 01:10:33PM +0100, Tobias Quathamer wrote: > Hi Sukhbir Singh, > > unfortunately, I cannot help you, because I'm facing the exact same > problem with the german variant. This is an old, long-standing bug[1] > which I'm still unable to solve. > > [1] https://bugs.launchpad.net/medicalterms/+bug/401423 -- 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/20130223143710.ge21...@an3as.eu
