[Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu?

[Tony Travis]

On 13/02/14 15:06, Jasmine Lognnes wrote:
> Dear Tony,
>
> That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit,
> and it exits with pasted in at the bottom. More complete output attached.
>
> What can you gather from this?

Hi, Jasmine.

Tim's advice is to run his upgrade script again if it crashes because of
broken dependencies. I use "aptitude" to correct any inconsistencies in
APT because it is good at fixing broken dependencies:

# get a root shell
sudo -i

# install aptitude
apt-get update
apt-get install aptitude

# fix broken dependencies
aptitude -f install

# make sure everything is up-to-date
aptitude dist-upgrade

# check if the package is available
apt-cache policy bio-linux-assembly-conversion-tools
bio-linux-assembly-conversion-tools:
  Installed: 0.01-10
  Candidate: 0.01-10
  Version table:
 *** 0.01-10 0
        500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64
Packages
        100 /var/lib/dpkg/status

# re-run Tim's script
bash bl_do_update_to7.sh

If you can't get it to work, check your APT configuration has the
attached files in it. If not, copy them in and update APT:

  aptitude update

I've upgraded quite a few Ubuntu servers to Bio-Linux using Tim's script
and it works quite well if you make sure you keep your APT consistent
using "aptitude" as I've described.

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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# Packages from PPA
deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main

# Packages from Bio-Linux main repo.  Note that adding this repo
# without the above PPA will result in some missing dependencies, so
# don't do that!
deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux

# Don't try to add a matching deb-src line to the above.  There is no
# source repo.  If we have source, it's in the PPA.
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deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/
deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/