[Bio-linux-list] 'Uninstalling' bio-linux

[Robert Evans]

Thanks a lot Tony!
Robert
 

    On Monday, May 30, 2016 5:31 PM, Tony Travis <tony.travis at abdn.ac.uk> wrote:
 

 On 31/05/16 01:06, Robert Evans wrote:
> Thanks Tony,
>
> I don't necessarily want to uninstall everything that isn't vanilla
> Ubuntu (I've installed various programs over the years), I just want to
> get the system set up in such a way that it will upgrade the core OS and
> utilities along the standard Ubuntu upgrade paths instead of the
> Biolinux/LTS upgrade paths.

Hi, Robert.

My script won't install/deinstall any packages - It just reports what
you would have to install/deinstall to reconcile differences between an
installed Bio-Linux (or Ubuntu) system and a list of packages based on
the 'manifest' file present on a 'live' Ubuntu DVD or another host.

> I don't know if your tool does that?  I'm quite happy manually
> uninstalling individual packages after deciding not to use them.

That's what my script is for: It will simply list the packages you have
installed that are not part of the 'vanilla' Ubuntu distribution. You
decide what to keep and what to uninstall - I wrote it to use with:

  dpkg --set-selections
  apt-get dselect-upgrade

However, now I use it to generate a list of packages for:

  apt install ...
  apt remove ...

> I've considered deselecting/deleting the Biolonux repositories in the
> Software Updater, and switching to upgrade to all new Ubuntu releases
> (not just LTS or the next Biolinux).  But I don't know if doing so will
> mangle things vis-a-vis any Biolinux updater scripts which may be in the
> system.

You will probably break a lot of packages if you do: It's advisable to
remove all your 'bio-linux*' packages before removing the repositories
or you risk dependency 'hell' :-(

> Would doing this solve the primary issue of being on a Biolinux upgrade
> path versus an Ubuntu upgrade path?

Yes, as long as you remove ALL your Bio-Linux packages before removing
the Bio-Linux repositories from your configuration.

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
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