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

[Troesemeier, Jan-Hendrik]

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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