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Re: "Could not perform immediate configuration" with debian-med

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 :-)


On Sun, Aug 7, 2011 at 6:26 PM, Steffen Möller <steffen_moeller@gmx.de> 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

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