Re: Status of BioRuby
On Sat, Oct 03, 2009 at 09:03:48PM -0400, John M Miller wrote: > I have done some translating from Perl to > Ruby and maybe I could just be a helper? That would be great. To get this issue a kick start I injected the current status of BioRuby to Debian Med SVN. In case anybody else of the Ruby team might step in and has commit rights if he is a Debian developer. Non Debian developers can be easily added to the project. John, I have not found you at alioth - I would welcome if you could register and I will add you to the Debian Med project. You might like to read the Debian Med policy[1]. I will update the packaging to the latest BioRuby version and apply our packaging policy regarding group maintenance. Once this is done I would be glad if you take over checking the Ruby specifics to make sure I have not broken anything. What do you think? Kind regards Andreas. [1] http://debian-med.alioth.debian.org/docs/policy.html -- 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
GNUmed / Debian-med Live CD
Hi all, Andreas has bugged me several times to get the Live CD stuff into SVN. I would like to discuss a few issues fist. The stuff I currently have produces a Live CD for GNUmed based on Debian Live. I could check that in but it is of limited use for Debian Med as a whole. In my view what needs to be done is to define package lists that can be fed to Debian Live's lh_config. These might overlap Debian Med's metapackages http://live.debian.net/manual/html/packages.html#package-installation For GNUmed one would simply use 'lh_config --packages "gnumed-client gnumed server"' 1) A good start for a Live CD is the Debian Live Task 'xfce'. It could be coupled with a package list that holds metapackages. Another option would be to define a set of tasks like 'xfce-emr' or 'xfce- biology' or whatnot. What do you think ? 2) The menus for GRUB and syslinux get autogenerated. For GNUmed I have cutomized the syslinux menu to allow for localized startup (the locales are created depending on your kernel parameters ). Those need to be preseeded in 'foo/bar/config/templates/syslinux/common/menu.cfg' 3) not all packages are in Debian Stable /Lenny. So a custom sources.list and apt preferences file needs to be supplied to pick up various software packages from testing. In short three things need to be done: 1) create a number of package lists to supply to lh_config 2) supply a sources.list 3) customize the menu If you want I could supply a working configuration to start out with but for a Debian-Med Live CD my config is too specific and needs work. Let me know how you want me to proceed. Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: GNUmed / Debian-med Live CD
Am Sonntag 04 Oktober 2009 15:58:54 schrieb Sebastian Hilbert: > Hi all, > My config to build a GNUmed Live CD on Debian Lenny with GNUmed packages from Unstable is available from http://www.gnumed.de/downloads/live-cd/developers/config10042009.tgz Sebastian > Andreas has bugged me several times to get the Live CD stuff into SVN. I > would like to discuss a few issues fist. > > The stuff I currently have produces a Live CD for GNUmed based on Debian > Live. I could check that in but it is of limited use for Debian Med as a > whole. > > In my view what needs to be done is to define package lists that can be fed > to Debian Live's lh_config. > > These might overlap Debian Med's metapackages > > http://live.debian.net/manual/html/packages.html#package-installation > > For GNUmed one would simply use 'lh_config --packages "gnumed-client gnumed > server"' > > 1) A good start for a Live CD is the Debian Live Task 'xfce'. It could be > coupled with a package list that holds metapackages. > > Another option would be to define a set of tasks like 'xfce-emr' or 'xfce- > biology' or whatnot. > > What do you think ? > > 2) The menus for GRUB and syslinux get autogenerated. For GNUmed I have > cutomized the syslinux menu to allow for localized startup (the locales are > created depending on your kernel parameters ). Those need to be preseeded > in 'foo/bar/config/templates/syslinux/common/menu.cfg' > > 3) not all packages are in Debian Stable /Lenny. So a custom sources.list > and apt preferences file needs to be supplied to pick up various software > packages from testing. > > In short three things need to be done: > 1) create a number of package lists to supply to lh_config > 2) supply a sources.list > 3) customize the menu > > If you want I could supply a working configuration to start out with but > for a Debian-Med Live CD my config is too specific and needs work. > > Let me know how you want me to proceed. > > Sebastian > -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: FreeDiams uploaded
Hi, I commited packaging stuff for FreeDiams which splits the single binary into two and also adds a doc packages. I'm not completely happy with this because when activating the rpath patch the dynamic libraries are not found in the end. This might be investigated later. I have a question with the upstream program: Is there really a need for asking the user to agree with the license? 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
Re: Status of BioRuby
On Sun, Oct 04, 2009 at 08:05:46PM -0400, John M Miller wrote: >> you at alioth - I would welcome if you could register > Done as jmmiller-guest. Welcome as a member of Debian Med team! ;-) >> and I will add you >> to the Debian Med project. You might like to read the Debian Med >> policy[1]. > Ok, looks like I need to refresh my memory about Subversion. Charles recently pointed[1] to a very helpful link how to deal with svn and ssh on Alioth.[2] So it might be sufficient to do svn checkout svn+ssh://jmmiller-gu...@svn.debian.org/svn/debian-med/trunk/packages/bioruby >> What do you think? > Right now I am thinking that I may not be as fast at this as you might > be hoping. Well, my packaging looks OK from a packaging perspective (except that some image files end up in /usr/lib instead of /usr/share, but that's rather nitpicking of lintian). The file layout in the new packages the same as in the old packages. I think it rather needs somebody to actually *test* the packages because I have no idea what to do here. If you think you (or anybody else) will not manage to test the result of my packaging stuff we might just go with the upload and wait for users reporting bugs. Kind regards and thanks for your offer to help in any case Andreas. [1] http://lists.debian.org/debian-med/2009/09/msg00116.html [2] http://wiki.debian.org/Alioth/SSH -- 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
Re: MUMmer patches and Artistic license.
On Sun, Jul 12, 2009 at 10:50:10PM +0900, Charles Plessy wrote: > Hi, thank you for the comment. > > I will stop to apply this patch until a better solution is found. Charles, could you please give an update of the status of mummer package? 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
Re: MUMmer patches and Artistic license.
Le Mon, Oct 05, 2009 at 08:41:05AM +0200, Andreas Tille a écrit : > On Sun, Jul 12, 2009 at 10:50:10PM +0900, Charles Plessy wrote: > > Hi, thank you for the comment. > > > > I will stop to apply this patch until a better solution is found. > > Charles, could you please give an update of the status of mummer package? Hi Andreas, Almost everything is done. There is a TODO point left in the changelog about restoring a renaming. Since MUMmer is released under the artistic license, we can not upload without double-checking that programs modified without the green light of Upstream are indeed renamed. The reason I have not done so is that I lost momentum when the upstream corrections for memory management took some time to come. Everybody is welcome to do the upload after clearing this TODO point. I plan to do this after uploading the bwa package that I prepared last week, for which I will ask for a copyright review on the debian-med list. The recent upload of infernal with incomplete copyright summary shows that we would benefit seeking from peer review on this file for new packages. 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
