Hi Steffen, I would say don't worry about backporting for me; I installed GBrowse by hand on the debian 5 server already, and if GBrowse will be available in the next Ubuntu, that's great, and I don't think there is a need to backport there either (the next ubuntu will be out in few months--why worry?) It will be nice for next year's summer workshop to just tell people to install GBrowse via apt-get in the ubuntu system we'll be using :-)
Thanks, Scott On Sun, Aug 7, 2011 at 6:26 PM, Steffen Möller <[email protected]> wrote: > Hello, great to hear from you on all this. Sorry for this bad experience with > the release mixing. You did not ruin your machine > now, I hope. > > Two and a half things come to mind (besides the updating of the server): > > a) we get those backports done > b) you get a chroot environment for gbrowse of a later Debian version > c) we just get it into the PPA for your current version of Ubuntu > > While I hope that Olivier will possibly try to think about a), Scott, please > read through c) for your current machine. And b), > well, would work. > > On 08/05/2011 11:30 PM, Olivier Sallou wrote: >> Hi andreas, >> backporting may be a huge tasks. I raised the point in a previous mail, but >> GBrowse depends on many perl modules and bioperl. >> Gbrowse by itself would be ok (I think), but bioperl stuff would be a pain I >> think.... > > Towards a) : Debian 5 about the same time as Lucid, I seem to recall. The > Debian Med PPA > https://launchpad.net/~debian-med/+archive/ppa has already seen BioPerl > 1.6.901-1~lucid1 uploaded by Charles. This fits with > gBrowse. If this is installable for Lenny, likely so, then Scott would be > half there. And we could look at bit more relaxed at > submitting such a package also for Debian's backports. I could do that, > actually. Olivier, would you not be tempted to try > building gBrowse on the PPA for Lucid? > > Towards b) : With tools like debootstrap one can install "unstable" into a > folder of "stable". "sudo chroot folder" will then > allow to install gbrowse without any extra hassle. All data and whatever > shall be shared needs to be "mount -o bind"ed into the > chroot, though. > > Towards c) : You can install the packages from Debian unstable also in a late > Ubuntu release. There are exceptions, but, hey, so. > you need to think hard to find them. gBrowse is in Ubuntu's Ocelot, not in > Natty and from my understanding it will not appear in > Natty or any earlier version of Ubuntu if not in some PPA like ours. What > version are you using? We can upload a package for that > version to the Debian Med PPA. But having a second look at > > https://launchpad.net/ubuntu/+source/gbrowse > http://packages.qa.debian.org/g/gbrowse.html > > https://launchpad.net/ubuntu/+source/bioperl > http://packages.qa.debian.org/b/bioperl.html > > I find all the packages to be platform independent. It might just work as it > is. So, for your current machine I think I would try > wget > https://launchpad.net/ubuntu/+source/gbrowse/2.38~dfsg-1/+build/2579699/+files/gbrowse_2.38~dfsg-1_all.deb > wget > https://launchpad.net/ubuntu/+source/gbrowse/2.38~dfsg-1/+build/2579699/+files/gbrowse-data_2.38~dfsg-1_all.deb > wget > https://launchpad.net/ubuntu/+source/gbrowse/2.38~dfsg-1/+build/2579699/+files/gbrowse-calign_2.38~dfsg-1_i386.deb > wget > https://launchpad.net/ubuntu/+source/bioperl/1.6.901-1/+build/2576037/+files/bioperl_1.6.901-1_all.deb > wget > https://launchpad.net/ubuntu/+source/bioperl/1.6.901-1/+build/2576037/+files/libbio-perl-perl_1.6.901-1_all.deb > > and then > sudo dpkg -i gbrowse*deb bioperl*deb libbio*deb > which will complain about missing Perl modules > sudo apt-get -f install > will try to fix that. And dpkg has a wonderful --force-all option. What is > missing or outdated please report and help yourself > with CRAN for that module. If this works, for your elderly server you may > prefer to take Charles' BioPerl package for Lucid over > the ones from above for Ocelot because of possibly less demanding > dependencies. > > Debian will get a PPA, too, soonish, so the mailing lists say. This is > excellent news. > > Steffen > > > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/ca+jtaowrf16vb9h4hxj-jiaf2ryycqpnmfpwozv6o4bo4er...@mail.gmail.com
