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

[Tim Booth]

Hi Jasmine,

Kudos to you for persisting on this.  APT is awesome when it works, but
infuriating when it doesn't.  As you've probably now realised, the
packages come in several categories:

bio-linux-* packages that you want to install
packages that come directly from Ubuntu
packages that sit in the Bio-Linux PPA
packages that come from other sources (eg. CRAN)
a few bio-linux-* packages that you probably don't want to install

I'm always trying to tidy up the situation by moving packages to the PPA
but some just won't go.  The big update script is supposed to sort it
all out for you in any case.

Your error is curious because you seem to be getting the "all"
architecture packages (artemis) but not the "amd64" packages
(assembly-conversion-tools).  You can see that
bio-linux-assembly-conversion tools really is there on the repo:

http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64/Packages

Normally I'd guess this means you have 32-bit Ubuntu but you say you
definitely have 64-bit installed.  Nevertheless it could be some APT
configuration issue that is stopping it picking up the binary packages.
Can you please send the output of:

apt-config dump

Cheers,

TIM

On Fri, 2014-02-14 at 12:51 +0000, 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?
> 
> Hugs,
> Jasmine =)
> 
> 
> 
> 
> 
> 
> 
> On 14 February 2014 13:38, Troesemeier, Jan-Hendrik
> <Jan-Hendrik.Troesemeier at pei.de> wrote:
> > Dear Jasmine,
> >
> > have you added the biolinux repositories (e.g. explained in http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository )? Afaik the missing package is a biolinux-repo only one.
> >
> > Cheers,
> > jan
> >
> > -----Ursprüngliche Nachricht-----
> > Von: Jasmine Lognnes [mailto:princess.jasmine.lognnes at gmail.com]
> > Gesendet: Freitag, 14. Februar 2014 11:29
> > An: Bio-Linux help and discussion
> > Cc: Bio-Linux technical discussion
> > Betreff: Re: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu?
> >
> > 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. What can you gather from this?
> >
> > Hugs,
> > Jasmine =)
> >
> >
> >
> > The following NEW packages will be installed:
> >   bio-linux-artemis
> > 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
> > Need to get 11.8 MB of archives.
> > After this operation, 47.7 MB of additional disk space will be used.
> > Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis.
> > (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.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-artemis (15.1.1-1) ...
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > E: Unable to locate package bio-linux-assembly-conversion-tools
> > Not all packages installed properly - exiting.
> >
> >
> >
> >
> >
> >
> >
> > On 12 February 2014 16:32, Tony Travis <tony.travis at abdn.ac.uk> wrote:
> >>
> >> On 12/02/14 15:03, Jasmine Lognnes wrote:
> >> > Dear Tim,
> >> >
> >> > That's a very impressive script. Wow!
> >> >
> >> > By going through the script I have cherry picked what looks like to
> >> > be needed on a plain Ubuntu 12.04 64bit. I have attached it as a script.
> >> > Can you verify that it is the correct procedure?
> >> >
> >> > On the liveUSB I did
> >> >
> >> > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}'
> >> >
> >> > and got the attached list of packages. On a successful installation,
> >> > should I end up these exact packages?
> >>
> >> Hi, Jasmine.
> >>
> >> I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu
> >> 12.04 LTS systems without any problems. You don't need to grep things
> >> out like you did. Just run the script in its entirety and please email
> >> any bug reports to the bio-linux-dev list.
> >>
> >> 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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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
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OX10 8BB 

http://nebc.nerc.ac.uk
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