<div dir="ltr"><div>Dear Brad,<br><br></div><div>Thanks for the input, and glad you agree. Yes, I've been following your work on bcbio-nextgen. It looks great!<br><br>Will keep working away at a minimal Bio-Linux container, and give updates on my progress here.<br><br>Cheers,<br><br>Steve<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 16 December 2014 at 14:32, Brad Chapman <span dir="ltr"><<a href="mailto:chapmanb@50mail.com" target="_blank">chapmanb@50mail.com</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Steve and Tony;<br>
I agree with this approach. This is essentially what we are doing with<br>
CloudBioLinux inside bcbio: providing a big ol' container with a lot of<br>
useful tools related to next-gen sequencing:<br>
<br>
<a href="https://github.com/chapmanb/bcbio-nextgen/blob/master/Dockerfile" target="_blank">https://github.com/chapmanb/bcbio-nextgen/blob/master/Dockerfile</a><br>
<br>
This uses both Bio-Linux and other installers like Homebrew cobbled<br>
together with CloudBioLinux.<br>
<br>
There is definitely an issue of size as you add more tools but if you<br>
want to run them together it's easier to manage and distribute a single<br>
instance rather than trying to chain multiple images. So somewhere in<br>
between a single tool and all the tools in the world is the right place<br>
to be. It would be cool to see what you can come up with for a Bio-Linux<br>
distribution,<br>
Brad<br>
<div><div class="h5"><br>
> Dear Tony,<br>
><br>
> I'm not wanting to create a full Bio-Linux installation in a container. As<br>
> you say, that would be contrary to the purpose of containers. I'm more<br>
> interested in creating a cut-down Bio-Linux-eqsue Docker image that has all<br>
> the relevant command line tools installed for undertaking bioinformatics<br>
> analyses, and access to the Bio-Linux 8 repos for installing additional<br>
> tools as necessary.<br>
><br>
> Another way of doing this would be to simply use the ubuntu base image, add<br>
> the Bio-Linux 8 repos, pin any GUI packages in apt with -1 priority, and<br>
> install all command line packages as part of the Dockerfile configuration.<br>
> Just trying to think of the easiest way to approach it.<br>
><br>
> I've followed Brad's work closely, so be interested to hear his take on<br>
> this too.<br>
><br>
> Cheers,<br>
><br>
> Steve<br>
><br>
> On 16 December 2014 at 12:00, <<a href="mailto:bio-linux-request@nebclists.nerc.ac.uk">bio-linux-request@nebclists.nerc.ac.uk</a>><br>
> wrote:<br>
>><br>
>> Message: 1<br>
>> Date: Mon, 15 Dec 2014 12:24:01 +0000<br>
>> From: Tony Travis <<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>><br>
>> To: <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>
>> Cc: Brad Chapman <<a href="mailto:chapmanb@50mail.com">chapmanb@50mail.com</a>><br>
>> Subject: Re: [Bio-Linux] BioLinux8 Dockerfile<br>
>> Message-ID: <<a href="mailto:548ED2E1.4050301@abdn.ac.uk">548ED2E1.4050301@abdn.ac.uk</a>><br>
>> Content-Type: text/plain; charset="windows-1252"<br>
>><br>
>> On 14/12/14 14:40, Booth, Timothy G. wrote:<br>
>> > [...]<br>
>> > To answer your question, I'd suggest the following approach - take a<br>
>> > fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and<br>
>> > X libs packages. Lots of packages that depend on them will be<br>
>> > removed. Then you can diff the master package list from the upgrade<br>
>> > script and the packages you have left on the system to get your<br>
>> > blacklist. I'm sure there are other approaches but this is the one<br>
>> > that springs to mind.<br>
>><br>
>> Hi, Tim and Steve.<br>
>><br>
>> I think you're missing the point about Docker if you're trying to create<br>
>> a Bio-Linux container. Docker is a lightweight container that relies on<br>
>> the host OS to provide kernel services and system daemons.<br>
>><br>
>> Bio-Linux is more appropriate as a host OS for Docker. I don't really<br>
>> see the point of trying to run a full Bio-linux in a Docker container<br>
>> because the overhead will be such that you might as well be using a VM.<br>
>><br>
>> Docker is most useful for providing an OS independent environment for<br>
>> applications like e.g. GATK that have specific version dependencies that<br>
>> are quite difficult to reconcile with versions of programs that are<br>
>> installed on a particular host. Docker provides portability of an<br>
>> application between host and OS's by encapsulating these dependencies.<br>
>><br>
>> Having said that, I'm currently trying to use Bio-Linux in a user-level<br>
>> "fakechroot" under 'Scientific' Linux (CentOS 6.3) on our HPC cluster<br>
>> because our out-sourced IT support company think Docker is too serious a<br>
>> security threat to be used on a 'production' server. I've pointed out<br>
>> that both AWS and Rackspace are offering Docker instances on their own<br>
>> cloud services 'securely'. I'm experimenting with Docker on my own PC.<br>
>><br>
>> [I've CC'ed this to Brad to get his take on using Docker for Bio-Linux]<br>
>><br>
>> Bye,<br>
>><br>
>> Tony.<br>
>><br>
><br>
> --<br>
><br>
> Steve Moss<br>
> <a href="http://about.me/gawbul" target="_blank">about.me/gawbul</a><br>
> [image: Steve Moss on <a href="http://about.me" target="_blank">about.me</a>]<br>
</div></div>> <<a href="http://about.me/gawbul" target="_blank">http://about.me/gawbul</a>><br>
</blockquote></div><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><a href="http://about.me/gawbul" style="margin:0px;padding:0px;border:0px;outline:0px;font-size:14px;vertical-align:baseline;color:rgb(43,130,173);text-decoration:none;line-height:18px" target="_blank"><font face="tahoma, sans-serif"></font><table border="0" cellpadding="0" cellspacing="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline;border-spacing:0px"><tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;vertical-align:baseline;height:30px"> </td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td align="left" valign="top" style="padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:top;line-height:1"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:bold;font-style:inherit;font-size:18px;vertical-align:baseline;line-height:1;color:rgb(51,51,51)">Steve Moss</div><div style="margin:3px 0px 0px;padding:0px;border:0px;outline:0px;font-style:inherit;font-size:12px;vertical-align:baseline">about.me/gawbul</div></td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td align="left" valign="top" style="padding:8px 0px 0px;border:0px;outline:0px;font-style:inherit;vertical-align:top;line-height:1"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline;text-align:right;background-color:rgb(197,208,224);height:4px"><img src="http://d13pix9kaak6wt.cloudfront.net/signature/colorbar.png" alt="Steve Moss on about.me" width="88" height="4" style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline;float:right;display:block"></div></td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-style:inherit;vertical-align:baseline"><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;vertical-align:baseline;height:20px"> </td></tr></tbody></table></a></div></div>
</div>