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