[Bio-Linux] BioLinux - sources.list

Brown, Stephen (AHVLA) Stephen.Brown at ahvla.gsi.gov.uk
Thu May 29 11:39:30 EDT 2014


Hi Tim,

Thank you for the quick reply,

Have just had a nose around the files in that directory and can see a host of other repo's. Including CRAN and FreeNX, will have a look at the contents and add to our mirror.list. Will make a note for Bio-Linux 8 to review the repo's again. Have been used to how CentOS and RHEL handle repo's with yum so just getting to grips with apt. 

Thanks again, will be able to get this setup now.

Thanks
Stephen

Stephen Brown
Scientific and Technical IT Services
Information Management and Technology
AHVLA Weybridge
T: +44 (0)1932 357879
F: +44 (0)1932 357 644
GTN: 3956 2879
E: stephen.brown at ahvla.gsi.gov.uk


-----Original Message-----
From: Tim Booth [mailto:tbooth at ceh.ac.uk] 
Sent: 29 May 2014 16:29
To: Bio-Linux help and discussion
Cc: Brown, Stephen (AHVLA)
Subject: Re: [Bio-Linux] BioLinux - sources.list

Hi Stephen,

Please join the mailing list to be sure of seeing all replies.

I think you're just missing that /etc/apt/sources.list.d/* is also incorporated into the mix.  In Ubuntu the sources.list tends to be auto-generated by the update manager and extra additions go into the list.d/ directory.

Your lines look fine apart from the "boil-linux" bit, but you may also want to mirror the CRAN repo and the FreeNX repo if you use that.

Note that I'm currently finishing and testing the script that upgrades you to Ubuntu 14.04/Bio-Linux 8.  That re-writes the sources configuration and adds the C2D4U repo of R modules so be aware you'll need to re-fix your settings after you upgrade.

Cheers,

TIM

On Thu, 2014-05-29 at 16:09 +0100, Brown, Stephen (AHVLA) wrote:
> Hi
> 
> Are you able to assist with a question around Biolinux and repo’s for 
> packages, we are looking to setup an internal mirror for our Biolinux 
> machines.
> 
> After checking in the /etc/apt/sources.list I cannot see any 
> references to any repo’s based at nebc.nerc.ac.uk, is this correct?
> When running an apt-get update I can see it is referencing 
> nebc.nerc.ac.uk, is this configuration stored somewhere else?
> 
> We would be looking to use apt-mirror to pull down the packages, do I 
> just need to add the following information into my mirror.list file?
> 
> Deb http://nebc.nerc.ac.uk/bio-linux/ unstable boil-linux
> 
> Deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
> 
> deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
> 
> Just as these are not present in the sources.list I am just a bit 
> confused how this is referencing the repo’s currently.
> 
> Thanks
> 
> Stephen
> 
> Stephen Brown
> 
>  
> 
> Animal Health and Veterinary Laboratories Agency (AHVLA)
> 
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>  
> 
> T: +44 (0)1932 357879
> 
> F: +44 (0)1932 357 644
> 
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> 
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> 
>  
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--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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OX10 8BB 

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