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

Tony Travis tony.travis at abdn.ac.uk
Mon Nov 28 07:32:37 EST 2016


On 01/11/16 00:15, Tim Booth wrote:
> Hi Burke, Tony, all,
>
> I'm delighted to see this discussion starting up regarding potentially
> re-invigorating Bio-Linux, or something inspired by it. Getting to grips
> with bioinformatics continues to be a trying experience for many
> biologists. The array of tools and technologies is bewildering; the
> learning curves steep. I firmly believe that providing an appealing,
> user friendly, pre-configured platform that can be put in front of
> complete beginners, yet with the power of a full-fledged Linux
> workstation, is a no-brainer in terms of overall return on investment.
> One or two dedicated developers, working in concert with the community,
> can effectively support hundreds if not thousands of users around the
> world. I hope people on this list will work with Tony to help him secure
> funding,  take up the reins, and build a developer community.
> [...]

Hi, Tim and Burke.

My main objective at present is to create Bio-Linux 9, based on Ubuntu
16.04 LTS, as soon as possible rather than completely re-factor the
Bio-Linux project. As Tim says, the main purpose of Bio-Linux is to
provide biologists with a pre-configured bioinformatics workstation that
can also be used by bioinformaticians for their work.

I'm not averse to 'containerization' of applications, but I see this as
a way of re-packaging upstream bioinformatics applications in a way that
avoids package dependency problems. I'm more concerned about the
problems caused by updating Bio-Linux systems with non-APT methods like
"pip", "cpan", "bioclite" and R itself from CRAN. In my experience, this
is what 'breaks' most things in Bio-Linux and one reason is that some
old Bio-Linux packages still put things into /usr/local - BAD!

So, although my plan might seem a bit pedestrian, I want to focus on
weeding out any use of /usr/local by Bio-Linux packages and getting
Bio-Linux 9 out of the door as soon as poss1ble.

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


The University of Aberdeen is a charity registered in Scotland, No SC013683.
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