From Stephen.Brown at ahvla.gsi.gov.uk Thu May 29 11:09:00 2014 From: Stephen.Brown at ahvla.gsi.gov.uk (Brown, Stephen (AHVLA)) Date: Thu, 29 May 2014 16:09:00 +0100 Subject: [Bio-Linux] BioLinux - sources.list Message-ID: 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) Scientific and Technical IT Services Information Management and Technology AHVLA Weybridge Woodham Lane New Haw Addlestone Surrey KT15 3NB T: +44 (0)1932 357879 F: +44 (0)1932 357 644 GTN: 3956 2879 E: stephen.brown at ahvla.gsi.gov.uk www.defra.gov.uk/ahvla Animal Health and Veterinary Laboratories Agency (AHVLA) This email and any attachments is intended for the named recipient only. If you have received it in error you have no authority to use, disclose, store or copy any of its contents and you should destroy it and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within AHVLA systems we can accept no responsibility once it has left our systems. Communications on AHVLA computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu May 29 11:29:23 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 29 May 2014 16:29:23 +0100 Subject: [Bio-Linux] BioLinux - sources.list In-Reply-To: References: Message-ID: <1401377363.20934.86.camel@balisaur> 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) > > Scientific and Technical IT Services > > Information Management and Technology > > AHVLA Weybridge > > Woodham Lane > > New Haw > > Addlestone > > Surrey > > KT15 3NB > > > > T: +44 (0)1932 357879 > > F: +44 (0)1932 357 644 > > GTN: 3956 2879 > > E: stephen.brown at ahvla.gsi.gov.uk > > > > www.defra.gov.uk/ahvla > > Animal Health and Veterinary Laboratories Agency (AHVLA) > > This email and any attachments is intended for the named recipient > only. > If you have received it in error you have no authority to use, > disclose, > store or copy any of its contents and you should destroy it and inform > the sender. > Whilst this email and associated attachments will have been checked > for known viruses whilst within AHVLA systems we can accept no > responsibility once it has left our systems. > Communications on AHVLA computer systems may be monitored and/or > recorded to secure the effective operation of the system and for other > lawful purposes. > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From Stephen.Brown at ahvla.gsi.gov.uk Thu May 29 11:39:30 2014 From: Stephen.Brown at ahvla.gsi.gov.uk (Brown, Stephen (AHVLA)) Date: Thu, 29 May 2014 16:39:30 +0100 Subject: [Bio-Linux] BioLinux - sources.list In-Reply-To: <1401377363.20934.86.camel@balisaur> References: <1401377363.20934.86.camel@balisaur> Message-ID: 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) > > Scientific and Technical IT Services > > Information Management and Technology > > AHVLA Weybridge > > Woodham Lane > > New Haw > > Addlestone > > Surrey > > KT15 3NB > > > > T: +44 (0)1932 357879 > > F: +44 (0)1932 357 644 > > GTN: 3956 2879 > > E: stephen.brown at ahvla.gsi.gov.uk > > > > www.defra.gov.uk/ahvla > > Animal Health and Veterinary Laboratories Agency (AHVLA) > > This email and any attachments is intended for the named recipient > only. > If you have received it in error you have no authority to use, > disclose, store or copy any of its contents and you should destroy it > and inform the sender. > Whilst this email and associated attachments will have been checked > for known viruses whilst within AHVLA systems we can accept no > responsibility once it has left our systems. > Communications on AHVLA computer systems may be monitored and/or > recorded to secure the effective operation of the system and for other > lawful purposes. > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705