[Bio-Linux] BioLinux/Ubuntu Package Manager Question

[Tim Booth]

Hi Christopher,

The short answer is you need a web proxy server, whatever the IT staff
say.

Without this, you could try to manually copy the updates as .deb files
from /var/cache/apt/archives on an on-line machine and install them on
the VMs with "sudo dpkg -i *.deb" but this is never going to be
practical if you want regular updates.  And it assumes that the updates
for the VMs and the on-line machine are identical, which they probably
aren't because you'll add and remove packages on different machines.

So really you need some sort of web proxy that permits the VMs to
retrieve package updates themselves.  The proxy only needs to permit
connections to the servers listed in sources.list, which you can list
like so (it varies depending on locale so I can't just paste the list):

cat /etc/apt/sources.list /etc/apt/sources.list.d/* | grep -o 'http[^ ]*' | sort -u

Can your IT people be persuaded that a web proxy only accessing a small
list of known servers is safe?  It does seem rather crazy to connect
your institute to the high-speed internet access you undoubtedly have
and then to spend your time shuttling files back and forth manually.

Hope that helps.

Cheers,

TIM

On Mon, 2013-09-16 at 18:08 +0100, Dubay, Christopher wrote:
> > To whom it may concern:
> 
> > 
> 
> > I had a question for you on the BioLinux/Ubuntu package manager.
> 
> > 
> 
> > A few of our BioLinux VMs are behind a firewall that is not allowing
> the package manager to find updates to the system.
> 
> > 
> 
> > What do you think would be the easiest way for us to get these VMs
> updated? We do have some machines that can access the Ubuntu and
> NEBC/NECR BioLinux repositories, so we could download the updates, but
> I don’t know enough Linux to know the best way to do this. Our IT
> staff gets nervous with using proxies, so a file transfer based method
> would be best.
> 
> > 
> 
> > Thanks in advance for your time responding to this query...
> 
> > 
> 
> > Christopher
> 
> > 
> 
> > Christopher Dubay, PhD
> 
> > Biomedical Informatics Team
> 
> > Immune Monitoring Laboratory
> 
> > Laboratory of Molecular and Tumor Immunology Earle A. Chiles
> Research
> 
> > Institute Providence Cancer Center
> 
> > 4805 NE Glisan St.- 2N57
> 
> > Portland, OR 97213  USA
> 
> > T: (503) 215-7981
> 
> > F: (503) 215-6841
> 
> > 
> 
> > christopher.dubay at providence.org
> 
> > 
> 
>  
> 
> 
> 
> 
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-- 
Tim Booth <tbooth at ceh.ac.uk>
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