[Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10

[Booth, Timothy G.]

hi,

(apologies for lack of caps i'm typing one-handed with my right hand in a plaster cast)

I do need to clean up the packages as there are some of the bio-linux-xxx ones that simply don't work in bl7, plus there are a few that will break bl6 that are installed on the dvd but are not yet in the repo. that should happen in the next week or so.  but in general if you see both bio-linux-emboss and emboss, say, you should install both as the emboss package is the core package from debian-med and the bio-linux-emboss package adds some extra bits.

you can find a full package manifest here, as well as the script to update from bl6 to bl7:

http://nebc.nerc.ac.uk/downloads/bl7_only/

running the bl_do_update_to7.sh script on a vanilla ubuntu 12.04 has been tested and should turn the ubuntu installation into bl7 for you.  i'm not sure how well it will work on a 12.10 release and i suspect a few packages will just refuse to install but i guess it wouldn't hurt to try if you are really keen to use 12.10.

cheers,

tim

________________________________________
From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Anthony Pemberton [A.J.Pemberton at bham.ac.uk]
Sent: 12 March 2013 15:05
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10

Jeremy,

The dependency problems probably arise from the fact that the BL7 programs (the debs) are designed to run on Ubuntu 12.04 – the LTS version. Try installing that version, then follow the instructions. I was able to do this (also with Mint Maya (13)),

Regards,

Tony P.


From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Martinson, Jeremy James
Sent: 12 March 2013 14:39
To: Bio Linux NEBC
Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10

Hi

Is there a preferred method for installing the BL7 programs on top of an existing Ubuntu installation? I have a workstation in my lab, and the Bio-Linux install DVD simply will not boot on it, no matter what I try. I can boot it from a standard Ubuntu 12.10 DVD though, and I've installed that instead, so now I'm trying to get BL7 up and running. I'm following the instructions on http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository but I'm running into a few dependency issues. Also, I notice that there are several packages that are present in both the bio-linux and Launchpad repositories (for example, emboss, paml, and qiime) - which one takes precedence? Any pointers would be much appreciated.

best regards

Jeremy

--
Dr. Jeremy Martinson
University of Pittsburgh
(412) 624-5646
jmartins at pitt.edu<mailto:jmartins at pitt.edu>


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