[Bio-Linux] BioLinux8 Dockerfile (Tony Travis)

[Steve Moss]

Dear Brad,

Thanks for the input, and glad you agree. Yes, I've been following your
work on bcbio-nextgen. It looks great!

Will keep working away at a minimal Bio-Linux container, and give updates
on my progress here.

Cheers,

Steve

On 16 December 2014 at 14:32, Brad Chapman <chapmanb at 50mail.com> wrote:
>
>
> Steve and Tony;
> I agree with this approach. This is essentially what we are doing with
> CloudBioLinux inside bcbio: providing a big ol' container with a lot of
> useful tools related to next-gen sequencing:
>
> https://github.com/chapmanb/bcbio-nextgen/blob/master/Dockerfile
>
> This uses both Bio-Linux and other installers like Homebrew cobbled
> together with CloudBioLinux.
>
> There is definitely an issue of size as you add more tools but if you
> want to run them together it's easier to manage and distribute a single
> instance rather than trying to chain multiple images. So somewhere in
> between a single tool and all the tools in the world is the right place
> to be. It would be cool to see what you can come up with for a Bio-Linux
> distribution,
> Brad
>
> > Dear Tony,
> >
> > I'm not wanting to create a full Bio-Linux installation in a container.
> As
> > you say, that would be contrary to the purpose of containers. I'm more
> > interested in creating a cut-down Bio-Linux-eqsue Docker image that has
> all
> > the relevant command line tools installed for undertaking bioinformatics
> > analyses, and access to the Bio-Linux 8 repos for installing additional
> > tools as necessary.
> >
> > Another way of doing this would be to simply use the ubuntu base image,
> add
> > the Bio-Linux 8 repos, pin any GUI packages in apt with -1 priority, and
> > install all command line packages as part of the Dockerfile
> configuration.
> > Just trying to think of the easiest way to approach it.
> >
> > I've followed Brad's work closely, so be interested to hear his take on
> > this too.
> >
> > Cheers,
> >
> > Steve
> >
> > On 16 December 2014 at 12:00, <bio-linux-request at nebclists.nerc.ac.uk>
> > wrote:
> >>
> >> Message: 1
> >> Date: Mon, 15 Dec 2014 12:24:01 +0000
> >> From: Tony Travis <tony.travis at abdn.ac.uk>
> >> To: <bio-linux at nebclists.nerc.ac.uk>
> >> Cc: Brad Chapman <chapmanb at 50mail.com>
> >> Subject: Re: [Bio-Linux] BioLinux8 Dockerfile
> >> Message-ID: <548ED2E1.4050301 at abdn.ac.uk>
> >> Content-Type: text/plain; charset="windows-1252"
> >>
> >> 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.
> >>
> >
> > --
> >
> > Steve Moss
> > about.me/gawbul
> > [image: Steve Moss on about.me]
> >   <http://about.me/gawbul>
>


-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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