[Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages

[Tony Travis]

On 27/05/16 14:54, Geert wrote:
> [...]
> PS.(now that I am writing an email anyways) I have already a good deal
> of programs on my computer that will be installed with Biolinux. Will
> that cause any difficulties.

Hi, Geert.

Sorry, I forgot to answer your question: I've got a lot of other
software installed on my Bio-Linux laptop and as long as you use the
Ubuntu package manager to install things you should not have any
problems. However, of you install things manually, you might break some
Bio-Linux packages. This is particularly true if you install R packages
from CRAN and Bioconductor manually to the same locations used by the
package manager. Similarly for perl and Python libraries installed using
CPAN and PiP. These are not Bio-Linux-specific problems, the conflicts
would happen in the same way on a standard Ubuntu system.

Bio-Linux has a historical problem about the use of /usr/local, which
package managers SHOULD NOT TOUCH but Bio-Linux does. This is because of
the way that some of the original bio-linux binary .deb packages were
created from conventional 'tarball' installations from source in
/usr/local, where software installed from 'tarballs" SHOULD be placed.
I've resolved this problem for my own putposes by creating
sub-directories in /usr/local and /opt for software I've installed
without the package manager, taking care not to overwrite anything that
Bio-Linux has put there. You can check what a .deb package installed:

  dpkg -L package_name

e.g.

> dpkg -L bio-linux-themes-v8
> /.
> /usr
> /usr/share
> /usr/share/gdm
> /usr/share/gdm/themes
> /usr/share/gdm/themes/bio-linux5
> /usr/share/gdm/themes/bio-linux5/screenshot.png
> /usr/share/gdm/themes/bio-linux5/GdmGreeterTheme.desktop
> /usr/share/gdm/themes/bio-linux5/quit.png
> /usr/share/gdm/themes/bio-linux5/dna-1400x1250.jpg
> /usr/share/gdm/themes/bio-linux5/options.png
> /usr/share/gdm/themes/bio-linux5/language.png
> ...

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


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