[Bio-linux-list] Bio-Linux Unity Desktop

[Tony Travis]

On 27/04/17 17:31, Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas wrote:
> Hi Tony,
>
> I'm all for MATE as well! The only downside I heard recently about MATE
> is that now with Ubuntu choosing GNOME 3 as the default there will be a
> lot of effort going to the gnome project. Not that this will kill MATE,
> but it will certainly  help improve GNOME 3 in the long run.

Hi, Raony.

You're right, and that's why I've been comparing Ubuntu-Gnome with
Ubuntu-MATE recently.

I've always advocated basing Bio-Linux on the main Ubuntu distro since I
ported it from Debian Sarge to Ubuntu 6.06 LTS, which used Gnome 2.
Since then, Tim has based all his Bio-Linux releases on the current
Ubuntu LTS distro. However, I've become increasingly aware that
Bio-Linux 8 does not run well on the type of low-spec. laptop that
people often bring with them to Bio-Linux courses. I'm more often
teaching Bio-Linux courses on 'cloud' VM's or terminal servers now and
installing a Windows or Mac "x2go" client on the laptops instead to
connect to a remote Bio-Linux MATE desktop.

> I like the approach of https://antergos.com which lets you choose the
> Desktop Environment you want during installation. The antergos installer
> was also a fork of Mate-welcome project which is something we should
> definitely plan to have for the Bioinformatics packages in Biolinux.
> Ubuntu is kind of outdated regarding this ...

Hmm... I'm not a big fan of "pacman" (the Arch Linux package manager).

One of the great things about basing Bio-Linux on Ubuntu is that it is,
at it's heart, Debian. That means we can use a HUGE range of packages,
including the fantastic work of Debian-Med who we've collaborated with
for packaging up-stream FLOSS bioinformatics software:

> https://www.debian.org/devel/debian-med/

The Debian-Med team have been a great help teaching us how to package
software and making their packages available as an Ubuntu PPA, which
allows packages to be installed in Ubuntu before they pass through all
the standard release stages into the Debian package repositories, used
by main-stream Ubuntu.

> Lastly, this is all free software, we are all an apt get install
> gnome/kde away from any other DE.
> The most important is to have lots of Bioinformatics packages available
> in a repository. That saves time!

Indeed, I installed the Gnome Desktop on my Bio-Linux laptop first to
check it out :-)

One thing I have to mention, although not about the MATE desktop, is
that I'm not opposed to 'rolling' upgrades. I found it very difficult to
get QIIME working when I upgraded my Bio-Linux laptop from Ubuntu 14.04
LTS to 16.04 LTS because of package-dependency-hell. I got out of this
particular hole by installing QIIME using Bioconda instead:

> https://bioconda.github.io/

QIIME is an example of great FLOSS, but it requires very specific
versions of supporting programs to be installed. We resolved this in
Bio-Linux by creating a 'wrapper' to invoke QIIME programs in the
correct environment, but Bioconda is a more effective solution and seems
to have quite a lot going for it!

Thanks for your comments,

  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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