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

[Tony Travis]

On 14/02/14 12:51, Jasmine Lognnes wrote:
> Dear Jan,
>
> The script added those for me, but looking at the repos in a browser,
> I can't see the bio-linux-assembly-conversion-tools in any of the
> repos. apt-cache search bio-linux | assembly doesn't give any hits
> either.
>
> However I see the package installed on the liveUSB stick. Have it been
> made from another repo?

Hi, Jasmine.

I'm using the sources.list fragment I sent you on my laptop "beluga":

> ajt at beluga:~$ cat /etc/apt/sources.list.d/nebc-bio-linux-precise.list
> # 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.

I've already got "bio-linux-assembly-conversion-tools" installed and
this is the APT policy for it:

> ajt at beluga:~$ 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

I can remove "bio-linux-assembly-conversion-tools" and re-install it
without any problems, so there is nothing wrong with the repository:

> ajt at beluga:~$ sudo aptitude purge bio-linux-assembly-conversion-tools
> The following packages will be REMOVED:
>   bio-linux-assembly-conversion-tools{p} bio-linux-staden{u}
> 0 packages upgraded, 0 newly installed, 2 to remove and 0 not upgraded.
> Need to get 0 B of archives. After unpacking 131 MB will be freed.
> Do you want to continue? [Y/n/?]
> (Reading database ... 847007 files and directories currently installed.)
> Removing bio-linux-assembly-conversion-tools ...
> Purging configuration files for bio-linux-assembly-conversion-tools ...
> (Reading database ... 846664 files and directories currently installed.)
> Removing bio-linux-staden ...
> Processing triggers for bamfdaemon ...
> Rebuilding /usr/share/applications/bamf.index...
> Processing triggers for desktop-file-utils ...
> Processing triggers for gnome-menus ...

This removed any cached copy of the package on my laptop:

> ajt at beluga:~$ sudo aptitude clean

Now, re-install from scratch:

> ajt at beluga:~$ sudo aptitude install bio-linux-assembly-conversion-tools
> The following NEW packages will be installed:
>   bio-linux-assembly-conversion-tools bio-linux-staden{a}
> 0 packages upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
> Need to get 52.3 MB of archives. After unpacking 131 MB will be used.
> Do you want to continue? [Y/n/?]
> Get: 1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-staden amd64 2006.1.7.0+1.11.6-7 [45.9 MB]
> Get: 2 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-assembly-conversion-tools amd64 0.01-10 [6,335 kB]
> Fetched 52.3 MB in 16s (3,154 kB/s)
> Selecting previously unselected package bio-linux-staden.
> (Reading database ... 843364 files and directories currently installed.)
> Unpacking bio-linux-staden (from .../bio-linux-staden_2006.1.7.0+1.11.6-7_amd64.deb) ...
> Selecting previously unselected package bio-linux-assembly-conversion-tools.
> Unpacking bio-linux-assembly-conversion-tools (from .../bio-linux-assembly-conversion-tools_0.01-10_amd64.deb) ...
> Processing triggers for bamfdaemon ...
> Rebuilding /usr/share/applications/bamf.index...
> Processing triggers for desktop-file-utils ...
> Processing triggers for gnome-menus ...
> Setting up bio-linux-staden (2006.1.7.0+1.11.6-7) ...
> Setting up bio-linux-assembly-conversion-tools (0.01-10) ...

Try installing it manually (i.e. not by running Tim's script):

  sudo -i
  apt-get update
  apt-get install aptitude
  aptitude -f install
  aptitude install bio-linux-assembly-conversion-tools

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.