[Bio-Linux] BioLinux8 Dockerfile

[Tony Travis]

On 14/12/14 14:40, Booth, Timothy G. wrote:
> [...]
> To answer your question, I'd suggest the following approach - take a
> fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and
> X libs packages.  Lots of packages that depend on them will be
> removed.  Then you can diff the master package list from the upgrade
> script and the packages you have left on the system to get your
> blacklist.  I'm sure there are other approaches but this is the one
> that springs to mind.

Hi, Tim and Steve.

I think you're missing the point about Docker if you're trying to create
a Bio-Linux container. Docker is a lightweight container that relies on
the host OS to provide kernel services and system daemons.

Bio-Linux is more appropriate as a host OS for Docker. I don't really
see the point of trying to run a full Bio-linux in a Docker container
because the overhead will be such that you might as well be using a VM.

Docker is most useful for providing an OS independent environment for
applications like e.g. GATK that have specific version dependencies that
are quite difficult to reconcile with versions of programs that are
installed on a particular host. Docker provides portability of an
application between host and OS's by encapsulating these dependencies.

Having said that, I'm currently trying to use Bio-Linux in a user-level
"fakechroot" under 'Scientific' Linux (CentOS 6.3) on our HPC cluster
because our out-sourced IT support company think Docker is too serious a
security threat to be used on a 'production' server. I've pointed out
that both AWS and Rackspace are offering Docker instances on their own
cloud services 'securely'. I'm experimenting with Docker on my own PC.

[I've CC'ed this to Brad to get his take on using Docker for Bio-Linux]

Bye,

  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


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