[Bio-linux-devel] Best method to build a regularly updated bioinformatics platform

[Tony Travis]

On 30/10/16 00:59, Squires, Richard (NIH/NIAID) [C] wrote:
> Hello all,
> 
>  
> 
> I am interested in hearing peoples’ thoughts about the best way to build
> a regularly updated platform for bioinformatics analysis and training.
> We are currently teaching classes on the NIH campus using Macs as well
> as at international locations, such as Mali and India, using Wintel
> laptops. We regularly have students who bring their own laptop and who
> would like to follow along with the lessons.

Hi, Richard.

I ran a Bio-Linux 8 training course at Assam Agricultural University in
Jorhat, India using the USB version of Bio-Linux 8. Everyone brought
their own laptop and although this was great for teaching Bio-Linux 8,
we ran more computationally demanding GWAS execises on a Bio-Linux 8
terminal server using the "x2go" client on the Bio-Linux 8 USB sticks as
well as showing people how to use the Windows or Mac "x2go" clients.

> To date, we have used Salt Scripts to update biolinux 8.0. with the
> software that we need. This has been used on the wintel laptops.
> Ideally, I would like to have a single workflow that would create a
> virtual machines or containers that can be used in the cloud or on a
> laptop, as well as scripts that can be used to install software on a mac
> or windows.

I'm not sure what you mean by "wintel" laptops: Do you mean dual-booted
with Windows or Bio-Linux or using a VM etc. I've just been trying out
the Ubuntu-in-Windows under the 'Anniversary' edition of Windows 10 :-)

My colleague Luca Beltrame uses "Salt" to manage our Bio-Linux 8 configs
for a project we are collaborating on in the Life Science Informatics
department at the Mario Negri Institure in Milan, Italy.

> I ask here because I think that this potential workflow could also be
> used to create a new version of biolinux that can be easily updated.

Bio-Linux can already be updated automatically from the Debian APT
repositories that it comes pre-configured with:

  apt update
  apt full-upgrade

This works well, but when Ubuntu 16.04 LTS was released quite a lot of
problems occurred for people trying to upgrade Bio-Linux 8 from Ubuntu
14.04 to 16.04 because some of the NERC packages (e.g. QIMME) have
dependencies for packages in the older release of Ubuntu.

I don't see how you get around problems like this unless you repackage
everything that breaks for the new Ubuntu release, which is what I've
started doing. I've now got Bio-Linux 8 running under Ubuntu 16.04 LTS,
but I've started work on a Bio-Linux 9 release, rather than explaining
the complicated work-arounds that are necessary to do the upgrade.

Bio-Linux 9 will be based on Ununtu 16.04 LTS

> Please let me know if you have any suggestions or questions.

I'm using Tim Booth's upgrade scripts and his instructions on GitHub
about how to create an iso of the new release:

  https://github.com/environmentalomics

I met Harry Mangalam at Basel Life Science Week recently and we
discussed at length how we could achieve what you are also trying to do,
which is create a supportable version of Bio-Linux. Harry teaches a
"Bio-Linux" course at UCI, but does not currently use NERC/EOS
Bio-Linux. Brad Chapman also used NERC/EOS Bio-Linux as the basis of
Cloud-Bio-Linux, and he is also a 'Docker' enthusiast.

I think it would be good if we start a collaboration to create a new
version of Bio-Linux and this list is a good place to discuss ideas.
Please forward this email to anyone else who might be interested and
let's try to put together a plan of action. I've CC'ed this off-list to
the people I've mentioned and also to Tracey Timms-Wilson, who is the
NERC/EOS project manager for Bio-Linux.

Thanks for raising this important topic,

  Tony.

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