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

[Robert Evans]

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.

I don't know if your tool does that?  I'm quite happy manually uninstalling individual packages after deciding not to use them.
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.
Would doing this solve the primary issue of being on a Biolinux upgrade path versus an Ubuntu upgrade path?

I guess I should have made this clearer initially.
Thanks,Robert
 

    On Monday, May 30, 2016 4:22 PM, Tony Travis <tony.travis at minke-informatics.co.uk> wrote:
 

 On 30/05/16 21:40, Robert Evans wrote:
> Hello,
> 
> I've had Biolinux on my personal computer for a few years but haven't
> used the bioinformatics programs.  I'd like to 'downgrade' to Ubuntu
> LTS, and then transition to the regular 6 month updates.
> 
> Is there a way I can do this without messing the system up?  Preferably
> also without having to reinstall the OS.

Hi, Robert.

I've got a script that will generate a list of packages to 'dselect':

> https://c6c327180cc0273ce5f218d003699c8b3cb652d4.googledrive.com/host/0B-h6GDwW40mtTEctZldjZG4xdTQ/

It compares the filesystem 'manifest' of a live DVD with the packages
that are installed on the local system, or the packages installed on two
different hosts e.g. Bio-Linux 8 on "wildcat" vs Ubuntu 14.04:

Extract the tar file and try it out like this:

> rwt017 at wildcat:~/Desktop/dpkg-dsel$ ./dpkg-dsel localhost ubuntu-14.04-desktop.sel
> abyss                        deinstall
> acacia                        deinstall
> account-plugin-windows-live                    install
> aglfn                        deinstall
> agrep                        deinstall
> alacarte                    deinstall
> amap-align                    deinstall
> ampliconnoise                    deinstall
> ant-gcj                        deinstall
> ant                        deinstall
> [...]
> xscreensaver-data                deinstall
> xscreensaver-gl                    deinstall
> xsltproc                    deinstall
> xtrans-dev                    deinstall
> xvnc4viewer                    deinstall
> zim                        deinstall
> zlib1g-dev                deinstall
> zlib1g:i386                    deinstall
> zsh-common                    deinstall
> zsh                        deinstall

This is a list of 'dselect-upgrade' package selections that should be
"installed" or "deinstalled": I use it to audit my Bio-Linux systems.

You can install it, and add any other package selections. You can also
use it to compare the package selections installed on two hosts e.g.

> rwt017 at wildcat:~/Desktop/dpkg-dsel$ ./dpkg-dsel localhost alleycat | head
> 3dm2                        install
> account-plugin-identica                install
> agrep                        deinstall
> alacarte                    deinstall
> ant-gcj                        deinstall
> antlr3                        deinstall
> ant-optional-gcj                deinstall
> apparmor-utils                    deinstall
> apport-symptoms                    deinstall
> attr                        deinstall
> [...]
> x11proto-xinerama-dev                deinstall
> xaw3dg:i386                    install
> xbrlapi                        deinstall
> xfonts-100dpi                    deinstall
> xfonts-75dpi                    deinstall
> xindy                        deinstall
> xindy-rules                    deinstall
> xscreensaver-data                deinstall
> xserver-xorg-lts-saucy                install
> zim                        deinstall

The results show how to change the first host to match the manifest
selections or the packages that are installed on the second host.

HTH,

  Tony.

-- 
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