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

[Jasmine Lognnes]

Dear Tony and Tim,

Thanks a lot for the very detailed help! The problem was indeed that
my other laptop were only 32bit, and that was the one where I ran the
upgrade script =) On my main laptop was where I tried to install all
the packages =)

So after a reinstall on the 64bit laptop, and running the upgrade
script, it worked perfectly.

Thanks a lot, and have a great weekend =)

Hugs,
Jasmine =)




On 14 February 2014 14:07, Tony Travis <tony.travis at abdn.ac.uk> wrote:
> 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.
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