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

[Sara Rassner]

Hi Tony,


I almost only use the terminal and do things in/from there, usually following a written protocol or a how-to guide. In that case it's not hard to find things as the protocols usually tell you what to type in. It's when I'm trying to find a program etc using the clicky-button approach that I get lost (since I rarely use Bio-Linux as an everyday computer).


Perhaps when the day comes and I start using a Linux computer more regularly that will stop being an issue. [😊]


(Oh and thanks for all the brilliant work on Bio-Linux by the way!)


Sara


________________________________
From: Bio-Linux-list <bio-linux-list-bounces at bioinformatics.org> on behalf of Tony Travis <tony.travis at minke-informatics.co.uk>
Sent: 27 April 2017 13:59
To: bio-linux-list at bioinformatics.org
Subject: Re: [Bio-linux-list] Bio-Linux Unity Desktop

On 27/04/17 14:31, Sara Rassner wrote:
> Hi,
>
>
> >An advantage of choosing
> >Ubuntu-MATE is that we would only need one set of training materials for
> >local and remote use of Bio-Linux and MATE requires considerably less
> >resources from the computer hardware than Gnome 3, which makes MATE more
> >suitable for running on older laptops or desktop computers.
>
>
> I think this is a very important consideration, since many of us are
> running Bio-Linux in VB on desktop PCs, so freeing up resources for the
> actual analysis is a good thing.

Hi, Sara.

I agree, and I debug Bio-Linux using a 'vanilla' install of the .ova in VB.

I also find that putting VB disk images on SSD makes a BIG difference to
performance!

> For users, like myself, who don't have that much experience with Linux
> and who are using Bio-Linux for bioinformatics only, it doesn't matter
> too much which desktop is used, as long as software and files can be
> easily found from the desktop. Personally, I prefer having both a menu
> tree and a search box, so that I can find everything even if I'm not
> sure where it is located or what it's called.

One problem that people I teach do find with Bio-Linux, or any Linux, is
that only the GUI programs are shown in the Unity Dash or on the
Gnome/MATE Menu and they don't know where the command-line programs are.
I've spent a lot of time trying to win the hearts and minds of Windows
users, but there is simply no alternative to running some programs from
the command-line and that's why I think that documentation is one of the
most important aspects of the Bio-Linux project. Half of the Bio-Linux
tutorial is dedicated to building a solid understanding of Linux, before
trying to do any bioinformatics.

The answer is, the command-line programs are on the PATH :-)

I think some problems that Windows users have with Linux can be resolved
by drawing an analogy between the Windows 'command' prompt and the Linux
shell. However, you're right that people need to be able to find things
easily. That's why we put local HTML documentation about all the
software, including command-line programs, into Bio-Linux. However, we
did not keep that documentation up-to-date as well as we should (I fixed
it on my installed Bio-Linux, but not on the .iso).

Thanks for your comments,

  Tony.

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