From tony.travis at minke-informatics.co.uk  Tue Apr 18 04:58:32 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 18 Apr 2017 09:58:32 +0100
Subject: [Bio-linux-list] FW: Upgrading Ubuntu version of BioLinux 8
In-Reply-To: <HE1PR0601MB2490E6022709DA3BB1EE22A1E5190@HE1PR0601MB2490.eurprd06.prod.outlook.com>
References: <CAAJF-1wZyF0wfoB2ZULH-ok2rRgyL3jskxcgZqpLUR_w5f5c_g@mail.gmail.com>
	<HE1PR0601MB2490E6022709DA3BB1EE22A1E5190@HE1PR0601MB2490.eurprd06.prod.outlook.com>
Message-ID: <b56dc66c-78c7-adb5-2b72-32347cb2de7a@minke-informatics.co.uk>

On 18/04/17 09:30, Timms-Wilson, Tracey wrote:
> *From:*Rajal Debnath [mailto:rajal.debnath at gmail.com]
> *Sent:* 14 April 2017 07:22
> *To:* Timms-Wilson, Tracey <tmt at ceh.ac.uk>
> *Subject:* Upgrading Ubuntu version of BioLinux 8
> [...]
> Dear Dr. Wilson,
> 
> I am writing this mail to enquire about the possibility of upgrading my
> BioLinux 8. First of all thanks to the entire team for the wonderful
> platform. I have been using the Biolinux 8 from a long time. However, I
> get frequent notifications to upgrade my Ubuntu version to 16.04 or to
> higher version in future.

Hi, Rajal.

Tracey has forwarded your email to me and I've CC'ed my reply to the
Bio-Linux mailing list in case anyone else has the same question.

It is possible to upgrade Bio-Linux 8 from Ubuntu 14.04 to 16.04 LTS,
but a lot of packages will break and you will need to do quite a lot of
work to resolve dependency problems.

> As I don?t see any new Biolinux versions being released could you please
> let me know if its ok to upgrade my current Ubuntu Operating system via
> the usual ubuntu upgrading system. Will it corrupt the existing system
> and its dependencies.

I've upgraded my own Bio-Linux laptop, and several Bio-Linux servers, to
Ubuntu 16.04 as part of my preparations to create Bio-Linux 9, but I
would not recommend doing the upgrade to Ubuntu 16.04 unless you are
prepared to fix a lot of dependency problems and do without packages
that depend on older Bio-Linux 8 packages that can't be installed under
Ubuntu 16.04 until those packages are upgraded.

If you do decide to go ahead, please post your experiences of upgrading
Bio-Linux 8 here so we can all help with the effort to create Bio-Linux
9 based on Ubuntu 16.04 LTS.

Thanks,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From tony.travis at minke-informatics.co.uk  Tue Apr 18 05:14:34 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 18 Apr 2017 10:14:34 +0100
Subject: [Bio-linux-list] FW: New contact form received
In-Reply-To: <HE1PR0601MB2490F0DC73AFCF9C6421AF49E5190@HE1PR0601MB2490.eurprd06.prod.outlook.com>
References: <951fea56e55329af1e81d25ec8aa5cda@environmentalomics.org>
	<HE1PR0601MB2490F0DC73AFCF9C6421AF49E5190@HE1PR0601MB2490.eurprd06.prod.outlook.com>
Message-ID: <390745f7-a589-f6cc-750b-c6bf84fc4fb7@minke-informatics.co.uk>

On 18/04/17 09:32, Timms-Wilson, Tracey wrote:
> 
> 
>> -----Original Message-----
>> From: Dhonghyo Kh [mailto:skycomingkho at gmail.com]
>> Sent: 13 April 2017 01:06
>> To: Timms-Wilson, Tracey <tmt at ceh.ac.uk>; Timms-Wilson, Tracey
>> <tmt at ceh.ac.uk>
>> Subject: New contact form received
>>
>>
>> You have received a new contact form message.
>> Name : Dhonghyo Kho
>> Email : skycomingkho at gmail.com
>> Message : I\'d like to know default system manager\'s password (?). After
>> installing bio-linux, I\'d like to change it to my password.

Hi, Dhonghyo.

Tracey has forwarded your email to me and I've CC'ed my reply to the
Bio-Linux mailing list in case anyone else has the same question.

The default user on the Bio-Linux 8 .ova, imported to VirtualBox or
VMwarePlayer, is "manager" with password "manager". See "Running
Bio-Linux as a VM with VirtualBox" at:

  http://environmentalomics.org/bio-linux-installation/

Please note that the .ova file is a pre-installed Bio-Linux image. If
you install from a DVD/USB created from the bio-linux-latest.iso file
then the default user is "live" during the installation process and this
user does not have a password. You create the initial Bio-Linux user
during the installation to disk and I recommend creating a nuser
"manager" as the administrator even on a single user Bio-Linux
installation and create a normal user account for yourself so you can
get in as "manager" if something goes wrong with your own account.

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From tony.travis at minke-informatics.co.uk  Thu Apr 20 09:01:44 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 20 Apr 2017 14:01:44 +0100
Subject: [Bio-linux-list] Test message - Please ignore
Message-ID: <a293ae4b-3baa-e172-9738-17f2fab186e8@minke-informatics.co.uk>

Hi,

This is a test message - Please ignore.

Thanks,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From tony.travis at minke-informatics.co.uk  Thu Apr 20 12:12:55 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 20 Apr 2017 17:12:55 +0100
Subject: [Bio-linux-list] Bug reports
Message-ID: <8fe556ef-32ae-a137-6578-9e4937962d7e@minke-informatics.co.uk>

Hi,

I'm preparing to do a 'point' release of Bio-Linux 8.0.8 and I need to
compile a list of all known bugs in Bio-Linux 8.0.7 so I can fix them.

One that I reported here previously is caused by '[arch=amd64]' missing
from the 'deb' entry in the "google-chrome.list" file, which prevents
"apt update" from working properly:

> diff -Naur /etc/apt/sources.list.d/.old/google-chrome.list.201502132202 /etc/apt/sources.list.d/google-chrome.list
> --- /etc/apt/sources.list.d/.old/google-chrome.list.201502132202	2015-02-13 22:02:32.695251288 +0000
> +++ /etc/apt/sources.list.d/google-chrome.list	2017-01-23 10:19:18.708833534 +0000
> @@ -1,3 +1,3 @@
>  ### THIS FILE IS AUTOMATICALLY CONFIGURED ###
>  # You may comment out this entry, but any other modifications may be lost.
> -deb http://dl.google.com/linux/chrome/deb/ stable main
> +deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main

Please post a Bug report here about any problems with the current
Bio-Linux 8.0.7 release (i.e. the "bio-linux-latest.iso" file).

Thanks,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From tony.travis at minke-informatics.co.uk  Thu Apr 27 08:55:55 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 27 Apr 2017 13:55:55 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
Message-ID: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>

Hi,

Bio-Linux 8 is based on Ubuntu 14.04 LTS Linux 'Unity' Desktop.

I want to know what Bio-Linux users think about the Bio-Linux Unity
Desktop, because Canonical (who develop Ubuntu) have announced that they
will no longer develop Unity and the next LTS release of Ubuntu will use
the Gnome 3 desktop instead as used in Ubuntu-Gnome:

> https://insights.ubuntu.com/2017/04/05/growing-ubuntu-for-cloud-and-iot-rather-than-phone-and-convergence/

Bio-Linux 8 already comes with the MATE desktop pre-installed for use on
a remote "x2go" desktop, when Bio-Linux 8 is used on a terminal server
or VM the cloud. However, the MATE desktop can also be used as the local
Bio-Linux desktop too, which has advantages for older laptops and PC's
with limited resources or servers with poor graphics hardware.

I've been evaluating Ubuntu-Gnome 16.04 and Ubuntu-MATE 16.04 as the
base-platform on which to create Bio-Linux 9. 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.

Unity will still be supported in 'maintenance' mode for the lifetime of
the Ubuntu 16.04 LTS release, but Ubuntu 18.04 LTS will use Gnome 3.

Please let me know what you think?

Thanks,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From brian at helix.biology.mcmaster.ca  Thu Apr 27 09:11:47 2017
From: brian at helix.biology.mcmaster.ca (Brian Golding)
Date: Thu, 27 Apr 2017 09:11:47 -0400
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <322caffbdad54989883ce8737e72206f@FHSHC2D11-2.csu.mcmaster.ca>
References: <322caffbdad54989883ce8737e72206f@FHSHC2D11-2.csu.mcmaster.ca>
Message-ID: <20170427131147.GA10938@helix.biology.mcmaster.ca>

I use both UNITY and KDE (by far, far perfer the later).

>From what you have written below sounds as though MATE is the easiest
choice but will it have the same lifetime?

Brian

       G. Brian Golding             E-mail: Golding at McMaster.CA
       Department of Biology        FAX: 905-522-6066
       McMaster University          Tel: 905-525-9140 ext 24829
       1280 Main Street West
       Hamilton, Ontario, L8S 4K1


On Thu, Apr 27, 2017 at 12:55:55PM +0000, Tony Travis wrote:
> Hi,
> 
> Bio-Linux 8 is based on Ubuntu 14.04 LTS Linux 'Unity' Desktop.
> 
> I want to know what Bio-Linux users think about the Bio-Linux Unity
> Desktop, because Canonical (who develop Ubuntu) have announced that they
> will no longer develop Unity and the next LTS release of Ubuntu will use
> the Gnome 3 desktop instead as used in Ubuntu-Gnome:
> 
> > https://insights.ubuntu.com/2017/04/05/growing-ubuntu-for-cloud-and-iot-rather-than-phone-and-convergence/
> 
> Bio-Linux 8 already comes with the MATE desktop pre-installed for use on
> a remote "x2go" desktop, when Bio-Linux 8 is used on a terminal server
> or VM the cloud. However, the MATE desktop can also be used as the local
> Bio-Linux desktop too, which has advantages for older laptops and PC's
> with limited resources or servers with poor graphics hardware.
> 
> I've been evaluating Ubuntu-Gnome 16.04 and Ubuntu-MATE 16.04 as the
> base-platform on which to create Bio-Linux 9. 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.
> 
> Unity will still be supported in 'maintenance' mode for the lifetime of
> the Ubuntu 16.04 LTS release, but Ubuntu 18.04 LTS will use Gnome 3.
> 
> Please let me know what you think?
> 
> Thanks,
> 
>   Tony.
> 
> -- 
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
> 

From mark.fernandes at ifr.ac.uk  Thu Apr 27 09:16:14 2017
From: mark.fernandes at ifr.ac.uk (mark fernandes (IFR))
Date: Thu, 27 Apr 2017 13:16:14 +0000
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
Message-ID: <AM5PR01MB29791C4750103A8912C7AE73C2100@AM5PR01MB2979.eurprd01.prod.exchangelabs.com>

Hi Tony,
	What you are suggesting (MATE for both) seems prudent (I'm an LXDE man myself which also works with X2Go)
	If you stuck with Unity - you'd only have to change the next time Bio-Linux was upgraded so maybe get the pain
	over and done now?
Regards,
Mark Fernandes                          

T:  +44 (0)1603 255000
Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK
www.ifr.ac.uk
Facebook | Twitter | LinkedIn | YouTube


The Institute of Food Research will be transforming into the Quadram Institute on 28th April 2017.
-----Original Message-----
From: Bio-Linux-list [mailto:bio-linux-list-bounces at bioinformatics.org] On Behalf Of Tony Travis
Sent: 27 April 2017 13:56
To: Bio-Linux mailing list <bio-linux-list at bioinformatics.org>
Subject: [Bio-linux-list] Bio-Linux Unity Desktop

Hi,

Bio-Linux 8 is based on Ubuntu 14.04 LTS Linux 'Unity' Desktop.

I want to know what Bio-Linux users think about the Bio-Linux Unity Desktop, because Canonical (who develop Ubuntu) have announced that they will no longer develop Unity and the next LTS release of Ubuntu will use the Gnome 3 desktop instead as used in Ubuntu-Gnome:

> https://insights.ubuntu.com/2017/04/05/growing-ubuntu-for-cloud-and-io
> t-rather-than-phone-and-convergence/

Bio-Linux 8 already comes with the MATE desktop pre-installed for use on a remote "x2go" desktop, when Bio-Linux 8 is used on a terminal server or VM the cloud. However, the MATE desktop can also be used as the local Bio-Linux desktop too, which has advantages for older laptops and PC's with limited resources or servers with poor graphics hardware.

I've been evaluating Ubuntu-Gnome 16.04 and Ubuntu-MATE 16.04 as the base-platform on which to create Bio-Linux 9. 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.

Unity will still be supported in 'maintenance' mode for the lifetime of the Ubuntu 16.04 LTS release, but Ubuntu 18.04 LTS will use Gnome 3.

Please let me know what you think?

Thanks,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
_______________________________________________
Bio-Linux-list mailing list
Bio-Linux-list at bioinformatics.org
http://www.bioinformatics.org/mm/listinfo/bio-linux-list

From mark.fernandes at ifr.ac.uk  Thu Apr 27 09:18:12 2017
From: mark.fernandes at ifr.ac.uk (mark fernandes (IFR))
Date: Thu, 27 Apr 2017 13:18:12 +0000
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
Message-ID: <AM5PR01MB29796B9E5D1CD00BB40BDDDFC2100@AM5PR01MB2979.eurprd01.prod.exchangelabs.com>

Hi Tony,
        What you are suggesting (MATE for both) seems prudent (I'm an LXDE man myself which also works with X2Go)
        If you stuck with Unity - you'd only have to change the next time Bio-Linux was upgraded so maybe get the pain
        over and done now?
Regards,
Mark Fernandes

T:  +44 (0)1603 255000
Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube
The Institute of Food Research will be transforming into the Quadram Institute on 28th April 2017.

-----Original Message-----
From: Bio-Linux-list [mailto:bio-linux-list-bounces at bioinformatics.org] On Behalf Of Tony Travis
Sent: 27 April 2017 13:56
To: Bio-Linux mailing list <bio-linux-list at bioinformatics.org>
Subject: [Bio-linux-list] Bio-Linux Unity Desktop

Hi,

Bio-Linux 8 is based on Ubuntu 14.04 LTS Linux 'Unity' Desktop.

I want to know what Bio-Linux users think about the Bio-Linux Unity Desktop, because Canonical (who develop Ubuntu) have announced that they will no longer develop Unity and the next LTS release of Ubuntu will use the Gnome 3 desktop instead as used in Ubuntu-Gnome:

> https://insights.ubuntu.com/2017/04/05/growing-ubuntu-for-cloud-and-io
> t-rather-than-phone-and-convergence/

Bio-Linux 8 already comes with the MATE desktop pre-installed for use on a remote "x2go" desktop, when Bio-Linux 8 is used on a terminal server or VM the cloud. However, the MATE desktop can also be used as the local Bio-Linux desktop too, which has advantages for older laptops and PC's with limited resources or servers with poor graphics hardware.

I've been evaluating Ubuntu-Gnome 16.04 and Ubuntu-MATE 16.04 as the base-platform on which to create Bio-Linux 9. 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.

Unity will still be supported in 'maintenance' mode for the lifetime of the Ubuntu 16.04 LTS release, but Ubuntu 18.04 LTS will use Gnome 3.

Please let me know what you think?

Thanks,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
_______________________________________________
Bio-Linux-list mailing list
Bio-Linux-list at bioinformatics.org
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From tony.travis at minke-informatics.co.uk  Thu Apr 27 09:25:26 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 27 Apr 2017 14:25:26 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <20170427131147.GA10938@helix.biology.mcmaster.ca>
References: <322caffbdad54989883ce8737e72206f@FHSHC2D11-2.csu.mcmaster.ca>
	<20170427131147.GA10938@helix.biology.mcmaster.ca>
Message-ID: <e0d9efe1-46ae-51b0-5192-ada8e63313c0@minke-informatics.co.uk>

On 27/04/17 14:11, Brian Golding wrote:
> I use both UNITY and KDE (by far, far perfer the later).
>
> >From what you have written below sounds as though MATE is the easiest
> choice but will it have the same lifetime?

Hi, Brian.

MATE is a fork of Gnome 2:

> https://mate-desktop.org/

It's widely supported across different Linux distro's, including Ubuntu:

> http://ubuntu-mate.org/

I know that Bio-Linux is used on low-spec laptops and desktops, and that
bandwidth constraints on remote desktops also impose limits on
performance. Unity, Gnome3 and KDE all require hardware graphics
acceleration to work properly. The Gnome 'Flashback' session, does not,
but it's performance is not good in comparison to MATE on the same system.

Have you tried running Bio-Linux 8 under KDE?

Thanks for your comments,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk

From tony.travis at minke-informatics.co.uk  Thu Apr 27 09:28:52 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 27 Apr 2017 14:28:52 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <AM5PR01MB29791C4750103A8912C7AE73C2100@AM5PR01MB2979.eurprd01.prod.exchangelabs.com>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5PR01MB29791C4750103A8912C7AE73C2100@AM5PR01MB2979.eurprd01.prod.exchangelabs.com>
Message-ID: <0bb0b756-4c04-a858-c934-53d10b92a5f6@minke-informatics.co.uk>

On 27/04/17 14:16, mark fernandes (IFR) wrote:
> Hi Tony,
>     What you are suggesting (MATE for both) seems prudent (I'm an LXDE
> man myself which also works with X2Go)
>     If you stuck with Unity - you'd only have to change the next time
> Bio-Linux was upgraded so maybe get the pain
>     over and done now?

Hi, Mark.

Yes, and that's the reason I'm asking people what they think about Unity.

Thanks for your comments,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk

From sararassner at hotmail.com  Thu Apr 27 09:31:24 2017
From: sararassner at hotmail.com (Sara Rassner)
Date: Thu, 27 Apr 2017 13:31:24 +0000
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
Message-ID: <AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>

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.


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.


Best wishes,

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 12:55
To: Bio-Linux mailing list
Subject: [Bio-linux-list] Bio-Linux Unity Desktop

Hi,

Bio-Linux 8 is based on Ubuntu 14.04 LTS Linux 'Unity' Desktop.

I want to know what Bio-Linux users think about the Bio-Linux Unity
Desktop, because Canonical (who develop Ubuntu) have announced that they
will no longer develop Unity and the next LTS release of Ubuntu will use
the Gnome 3 desktop instead as used in Ubuntu-Gnome:

> https://insights.ubuntu.com/2017/04/05/growing-ubuntu-for-cloud-and-iot-rather-than-phone-and-convergence/

Bio-Linux 8 already comes with the MATE desktop pre-installed for use on
a remote "x2go" desktop, when Bio-Linux 8 is used on a terminal server
or VM the cloud. However, the MATE desktop can also be used as the local
Bio-Linux desktop too, which has advantages for older laptops and PC's
with limited resources or servers with poor graphics hardware.

I've been evaluating Ubuntu-Gnome 16.04 and Ubuntu-MATE 16.04 as the
base-platform on which to create Bio-Linux 9. 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.

Unity will still be supported in 'maintenance' mode for the lifetime of
the Ubuntu 16.04 LTS release, but Ubuntu 18.04 LTS will use Gnome 3.

Please let me know what you think?

Thanks,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
Minke Informatics Limited Home<http://minke-informatics.co.uk/>
minke-informatics.co.uk
Address: Location: Contact: Publications: 3 Donview Bridge of Alford Scotland (UK) AB33 8QJ: View the map +44 07985 078324 tony.travis at minke-informatics.co.uk


mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
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From tony.travis at minke-informatics.co.uk  Thu Apr 27 09:59:57 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 27 Apr 2017 14:59:57 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
Message-ID: <922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>

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.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk

From sararassner at hotmail.com  Thu Apr 27 10:24:17 2017
From: sararassner at hotmail.com (Sara Rassner)
Date: Thu, 27 Apr 2017 14:24:17 +0000
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>,
	<922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>
Message-ID: <AM5P189MB0580754D6130E8A246D16FFAA4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>

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.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
Minke Informatics Limited Home<http://minke-informatics.co.uk/>
minke-informatics.co.uk
Address: Location: Contact: Publications: 3 Donview Bridge of Alford Scotland (UK) AB33 8QJ: View the map +44 07985 078324 tony.travis at minke-informatics.co.uk


mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk
_______________________________________________
Bio-Linux-list mailing list
Bio-Linux-list at bioinformatics.org
http://www.bioinformatics.org/mm/listinfo/bio-linux-list
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From tony.travis at minke-informatics.co.uk  Thu Apr 27 10:48:55 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 27 Apr 2017 15:48:55 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <AM5P189MB0580754D6130E8A246D16FFAA4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>
	<AM5P189MB0580754D6130E8A246D16FFAA4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
Message-ID: <bc6ddbe9-8a26-3dc8-937f-61a2423d2c8c@minke-informatics.co.uk>

On 27/04/17 15:24, Sara Rassner wrote:
> 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).

Hi, Sara.

Ah! clicky-buttons - You either love 'em or you hate 'em :-)

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

Actually, I've been trying out the Microsoft/Ubuntu "bash" shell, which
might be a another way of running command-line 'Linux' programs if you
really prefer to work in a Windows environement:

> https://msdn.microsoft.com/en-gb/commandline/wsl/about

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

Thanks, but I can't claim all of the credit for Bio-Linux :-)

Tim Booth was the lead developer of Bio-Linux until, he left the project
for a new job, but I have been involved in the Bio-Linux project helping
Tim for many years. I'm now seeking funding to develop Bio-Linux 9 and
Dawn Field, who lead the original NERC/EOS Bio-Linux project from the
outset is also looking for ways to develop Bio-Linux further. We plan to
coordinate our efforts with Steve Moss at "bioinformatics.org", where
this Bio-Linux list is being served from:

> https://www.bioinformatics.org/groups/?group_id=341

Glad you find Bio-Linux useful!

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk

From maxime.gommeaux at univ-reims.fr  Thu Apr 27 11:04:41 2017
From: maxime.gommeaux at univ-reims.fr (Maxime GOMMEAUX)
Date: Thu, 27 Apr 2017 17:04:41 +0200
Subject: [Bio-linux-list] Bio-Linux-list Digest, Vol 22, Issue 2
In-Reply-To: <mailman.2785.1493299890.4761.bio-linux-list@bioinformatics.org>
References: <mailman.2785.1493299890.4761.bio-linux-list@bioinformatics.org>
Message-ID: <cdb14b47-13d4-9652-7619-47952c392d11@univ-reims.fr>

Hi Tony,

I don't really have an opinion about Unity. I find this desktop 
convenient and easy to use, but I also liked GNOME when I used it quite 
some time ago. I have very limited experience with MATE (only from the 
live distro-astro) but I guess it would also fulfil my needs!

So I wouldn't mind if the future Bio-Linux uses MATE.

Yours,
Maxime

From mkmodi at aau.ac.in  Thu Apr 27 11:08:40 2017
From: mkmodi at aau.ac.in (Mahendra Modi)
Date: Thu, 27 Apr 2017 20:38:40 +0530
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <bc6ddbe9-8a26-3dc8-937f-61a2423d2c8c@minke-informatics.co.uk>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>
	<AM5P189MB0580754D6130E8A246D16FFAA4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<bc6ddbe9-8a26-3dc8-937f-61a2423d2c8c@minke-informatics.co.uk>
Message-ID: <CAPUhUGw4eV846E_gYZaCe8A=2phh_WvDMDVrdwZeS+F0JFBJTg@mail.gmail.com>

Tony,

Most of the people in our lab remotely connect to the biolinux server on
using x2go and hence uses Mate desktop. As such, using Mate for both local
as well as remote desktop seems to be a very good idea to me.

Mahendra

Mahendra K Modi

On Apr 27, 2017 20:19, "Tony Travis" <tony.travis at minke-informatics.co.uk>
wrote:

> On 27/04/17 15:24, Sara Rassner wrote:
> > 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).
>
> Hi, Sara.
>
> Ah! clicky-buttons - You either love 'em or you hate 'em :-)
>
> > Perhaps when the day comes and I start using a Linux computer more
> > regularly that will stop being an issue. ?
>
> Actually, I've been trying out the Microsoft/Ubuntu "bash" shell, which
> might be a another way of running command-line 'Linux' programs if you
> really prefer to work in a Windows environement:
>
> > https://msdn.microsoft.com/en-gb/commandline/wsl/about
>
> > (Oh and thanks for all the brilliant work on Bio-Linux by the way!)
>
> Thanks, but I can't claim all of the credit for Bio-Linux :-)
>
> Tim Booth was the lead developer of Bio-Linux until, he left the project
> for a new job, but I have been involved in the Bio-Linux project helping
> Tim for many years. I'm now seeking funding to develop Bio-Linux 9 and
> Dawn Field, who lead the original NERC/EOS Bio-Linux project from the
> outset is also looking for ways to develop Bio-Linux further. We plan to
> coordinate our efforts with Steve Moss at "bioinformatics.org", where
> this Bio-Linux list is being served from:
>
> > https://www.bioinformatics.org/groups/?group_id=341
>
> Glad you find Bio-Linux useful!
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548 http://minke-informatics.co.uk
> mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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From tony.travis at minke-informatics.co.uk  Thu Apr 27 11:25:11 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 27 Apr 2017 16:25:11 +0100
Subject: [Bio-linux-list] Bio-Linux-list Digest, Vol 22, Issue 2
In-Reply-To: <cdb14b47-13d4-9652-7619-47952c392d11@univ-reims.fr>
References: <mailman.2785.1493299890.4761.bio-linux-list@bioinformatics.org>
	<cdb14b47-13d4-9652-7619-47952c392d11@univ-reims.fr>
Message-ID: <daaa8137-bcd6-5047-6378-ccbce9cad8aa@minke-informatics.co.uk>

On 27/04/17 16:04, Maxime GOMMEAUX wrote:
> Hi Tony,
>
> I don't really have an opinion about Unity. I find this desktop
> convenient and easy to use, but I also liked GNOME when I used it quite
> some time ago. I have very limited experience with MATE (only from the
> live distro-astro) but I guess it would also fulfil my needs!
>
> So I wouldn't mind if the future Bio-Linux uses MATE.

Hi, Maxime.

In fact, MATE is a fork of Gnome 2 and if you used Gnome quite some time
ago then you were probably using Gnome 2.

The reason MATE was forked from Gnome 2 is that the Gnome developers
decided to completely redesign Gnome, but many people don't like the
Gnome 3 they have produced. I've not looked at Gnome 3 seriously until
just recently, because I normally run Bio-Linux on a terminal server or
in a 'cloud' VM using a MATE desktop via "x2go". Gnome 3 is very different.

I compared Ubuntu-Gnome 16.04 LTS and Ubuntu-Mate 16.04 LTS on my laptop
(Intel i5, 8GiB RAM and Radeon graphics).

Thanks for your comments,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk

From tony.travis at minke-informatics.co.uk  Thu Apr 27 11:26:27 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 27 Apr 2017 16:26:27 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <CAPUhUGw4eV846E_gYZaCe8A=2phh_WvDMDVrdwZeS+F0JFBJTg@mail.gmail.com>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>
	<AM5P189MB0580754D6130E8A246D16FFAA4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<bc6ddbe9-8a26-3dc8-937f-61a2423d2c8c@minke-informatics.co.uk>
	<CAPUhUGw4eV846E_gYZaCe8A=2phh_WvDMDVrdwZeS+F0JFBJTg@mail.gmail.com>
Message-ID: <47e8c318-98d4-ceb0-9513-d7316f9a5935@minke-informatics.co.uk>

On 27/04/17 16:08, Mahendra Modi wrote:
> Tony,
>
> Most of the people in our lab remotely connect to the biolinux server on
> using x2go and hence uses Mate desktop. As such, using Mate for both
> local as well as remote desktop seems to be a very good idea to me.

Hi, Mahendra

Good to know - Thanks for your comments,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk

From raonyguimaraes at gmail.com  Thu Apr 27 12:31:12 2017
From: raonyguimaraes at gmail.com (=?UTF-8?Q?Raony_Guimaraes_Corr=C3=AAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Thu, 27 Apr 2017 17:31:12 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <47e8c318-98d4-ceb0-9513-d7316f9a5935@minke-informatics.co.uk>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>
	<AM5P189MB0580754D6130E8A246D16FFAA4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<bc6ddbe9-8a26-3dc8-937f-61a2423d2c8c@minke-informatics.co.uk>
	<CAPUhUGw4eV846E_gYZaCe8A=2phh_WvDMDVrdwZeS+F0JFBJTg@mail.gmail.com>
	<47e8c318-98d4-ceb0-9513-d7316f9a5935@minke-informatics.co.uk>
Message-ID: <CALenahmd0VtZE=Tt5j6NAh-Y+vUaisTTrkhbwV7HznSgYchwzQ@mail.gmail.com>

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.

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 ...

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!

Kind Regards.

On 27 Apr 2017 4:26 p.m., "Tony Travis" <tony.travis at minke-informatics.co.uk>
wrote:

> On 27/04/17 16:08, Mahendra Modi wrote:
> > Tony,
> >
> > Most of the people in our lab remotely connect to the biolinux server on
> > using x2go and hence uses Mate desktop. As such, using Mate for both
> > local as well as remote desktop seems to be a very good idea to me.
>
> Hi, Mahendra
>
> Good to know - Thanks for your comments,
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548 http://minke-informatics.co.uk
> mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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From tony.travis at abdn.ac.uk  Thu Apr 27 15:01:04 2017
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 27 Apr 2017 20:01:04 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <CALenahmd0VtZE=Tt5j6NAh-Y+vUaisTTrkhbwV7HznSgYchwzQ@mail.gmail.com>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<AM5P189MB05800B22AE0E77059F55F149A4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<922c1087-3543-f27c-6e28-bc96567ba28c@minke-informatics.co.uk>
	<AM5P189MB0580754D6130E8A246D16FFAA4100@AM5P189MB0580.EURP189.PROD.OUTLOOK.COM>
	<bc6ddbe9-8a26-3dc8-937f-61a2423d2c8c@minke-informatics.co.uk>
	<CAPUhUGw4eV846E_gYZaCe8A=2phh_WvDMDVrdwZeS+F0JFBJTg@mail.gmail.com>
	<47e8c318-98d4-ceb0-9513-d7316f9a5935@minke-informatics.co.uk>
	<CALenahmd0VtZE=Tt5j6NAh-Y+vUaisTTrkhbwV7HznSgYchwzQ@mail.gmail.com>
Message-ID: <a806c5dd-6998-6b5b-6f7b-46387ca69351@abdn.ac.uk>

On 27/04/17 17:31, Raony Guimaraes Corr?a 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.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

From Simon.Wagstaff at lstmed.ac.uk  Fri Apr 28 10:24:59 2017
From: Simon.Wagstaff at lstmed.ac.uk (Simon Wagstaff)
Date: Fri, 28 Apr 2017 14:24:59 +0000
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
Message-ID: <VI1PR04MB1389F50CBCDC4161140843ADAE130@VI1PR04MB1389.eurprd04.prod.outlook.com>

Hi Tony,
Thanks for the email. I would default to MATE on both for the reasons you describe - limitations on graphical hardware and consistency of documentation.

Many of the students we teach using Biolinux-X2GO-MATE quickly gain confidence and go on to install Biolinux on their own hardware.

Cheers,

Simon

_________________________________

Simon Wagstaff PhD
Head of Scientific Computing
Liverpool School of Tropical Medicine
Pembroke Place, Liverpool, L3 5QA UK

Tel: +44-(0)151-705-3164
Fax: +44-(0)151-705-3371
email: simon.wagstaff at lstmed.ac.uk
http://www.lstmed.ac.uk/research/departments/staff-profiles/simon-wagstaff


-----Original Message-----
From: Bio-Linux-list [mailto:bio-linux-list-bounces at bioinformatics.org] On Behalf Of Tony Travis
Sent: 27 April 2017 13:56
To: Bio-Linux mailing list <bio-linux-list at bioinformatics.org>
Subject: [Bio-linux-list] Bio-Linux Unity Desktop

Hi,

Bio-Linux 8 is based on Ubuntu 14.04 LTS Linux 'Unity' Desktop.

I want to know what Bio-Linux users think about the Bio-Linux Unity Desktop, because Canonical (who develop Ubuntu) have announced that they will no longer develop Unity and the next LTS release of Ubuntu will use the Gnome 3 desktop instead as used in Ubuntu-Gnome:

> https://insights.ubuntu.com/2017/04/05/growing-ubuntu-for-cloud-and-io
> t-rather-than-phone-and-convergence/

Bio-Linux 8 already comes with the MATE desktop pre-installed for use on a remote "x2go" desktop, when Bio-Linux 8 is used on a terminal server or VM the cloud. However, the MATE desktop can also be used as the local Bio-Linux desktop too, which has advantages for older laptops and PC's with limited resources or servers with poor graphics hardware.

I've been evaluating Ubuntu-Gnome 16.04 and Ubuntu-MATE 16.04 as the base-platform on which to create Bio-Linux 9. 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.

Unity will still be supported in 'maintenance' mode for the lifetime of the Ubuntu 16.04 LTS release, but Ubuntu 18.04 LTS will use Gnome 3.

Please let me know what you think?

Thanks,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
_______________________________________________
Bio-Linux-list mailing list
Bio-Linux-list at bioinformatics.org
http://www.bioinformatics.org/mm/listinfo/bio-linux-list
________________________________


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This e-mail message is sent on behalf of the Liverpool School of Tropical Medicine, a charitable company limited by guarantee registered in England and Wales with company number 222655 and whose registered office is at Pembroke Place Liverpool L3 5QA ("LSTM")

The contents of this e-mail are subject to LSTM?s email disclaimer found at:
http://www.lstmed.ac.uk/disclaimer/email-disclaimer

From briancady101 at yahoo.com  Fri Apr 28 16:02:31 2017
From: briancady101 at yahoo.com (Brian Cady)
Date: Fri, 28 Apr 2017 20:02:31 +0000 (UTC)
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <VI1PR04MB1389F50CBCDC4161140843ADAE130@VI1PR04MB1389.eurprd04.prod.outlook.com>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<VI1PR04MB1389F50CBCDC4161140843ADAE130@VI1PR04MB1389.eurprd04.prod.outlook.com>
Message-ID: <195171347.7141959.1493409751299@mail.yahoo.com>

I vote for MATE, with it's better compatibility with older machines.
Brian
 

    On Friday, April 28, 2017 10:25 AM, Simon Wagstaff <Simon.Wagstaff at lstmed.ac.uk> wrote:
 

 Hi Tony,
Thanks for the email. I would default to MATE on both for the reasons you describe - limitations on graphical hardware and consistency of documentation.

Many of the students we teach using Biolinux-X2GO-MATE quickly gain confidence and go on to install Biolinux on their own hardware.

Cheers,

Simon

_________________________________

Simon Wagstaff PhD
Head of Scientific Computing
Liverpool School of Tropical Medicine
Pembroke Place, Liverpool, L3 5QA UK

Tel: +44-(0)151-705-3164
Fax: +44-(0)151-705-3371
email: simon.wagstaff at lstmed.ac.uk
http://www.lstmed.ac.uk/research/departments/staff-profiles/simon-wagstaff


-----Original Message-----
From: Bio-Linux-list [mailto:bio-linux-list-bounces at bioinformatics.org] On Behalf Of Tony Travis
Sent: 27 April 2017 13:56
To: Bio-Linux mailing list <bio-linux-list at bioinformatics.org>
Subject: [Bio-linux-list] Bio-Linux Unity Desktop

Hi,

Bio-Linux 8 is based on Ubuntu 14.04 LTS Linux 'Unity' Desktop.

I want to know what Bio-Linux users think about the Bio-Linux Unity Desktop, because Canonical (who develop Ubuntu) have announced that they will no longer develop Unity and the next LTS release of Ubuntu will use the Gnome 3 desktop instead as used in Ubuntu-Gnome:

> https://insights.ubuntu.com/2017/04/05/growing-ubuntu-for-cloud-and-io
> t-rather-than-phone-and-convergence/

Bio-Linux 8 already comes with the MATE desktop pre-installed for use on a remote "x2go" desktop, when Bio-Linux 8 is used on a terminal server or VM the cloud. However, the MATE desktop can also be used as the local Bio-Linux desktop too, which has advantages for older laptops and PC's with limited resources or servers with poor graphics hardware.

I've been evaluating Ubuntu-Gnome 16.04 and Ubuntu-MATE 16.04 as the base-platform on which to create Bio-Linux 9. 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.

Unity will still be supported in 'maintenance' mode for the lifetime of the Ubuntu 16.04 LTS release, but Ubuntu 18.04 LTS will use Gnome 3.

Please let me know what you think?

Thanks,

? Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548? ? ? ? ? ? ? ? ? ? http://minke-informatics.co.uk
mob. +44(0)7985 078324? ? ? ? mailto:tony.travis at minke-informatics.co.uk
_______________________________________________
Bio-Linux-list mailing list
Bio-Linux-list at bioinformatics.org
http://www.bioinformatics.org/mm/listinfo/bio-linux-list
________________________________


[http://www.lstmed.ac.uk/sites/default/files/lstm_email_logo.gif]

This e-mail message is sent on behalf of the Liverpool School of Tropical Medicine, a charitable company limited by guarantee registered in England and Wales with company number 222655 and whose registered office is at Pembroke Place Liverpool L3 5QA ("LSTM")

The contents of this e-mail are subject to LSTM?s email disclaimer found at:
http://www.lstmed.ac.uk/disclaimer/email-disclaimer
_______________________________________________
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Bio-Linux-list at bioinformatics.org
http://www.bioinformatics.org/mm/listinfo/bio-linux-list


   
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From tony.travis at minke-informatics.co.uk  Sat Apr 29 19:07:05 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Sun, 30 Apr 2017 00:07:05 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <VI1PR04MB1389F50CBCDC4161140843ADAE130@VI1PR04MB1389.eurprd04.prod.outlook.com>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<VI1PR04MB1389F50CBCDC4161140843ADAE130@VI1PR04MB1389.eurprd04.prod.outlook.com>
Message-ID: <53a4b979-1d4f-da21-7c4a-d41143796bf7@minke-informatics.co.uk>

On 28/04/17 15:24, Simon Wagstaff wrote:
> Hi Tony, Thanks for the email. I would default to MATE on both for
> the reasons you describe - limitations on graphical hardware and
> consistency of documentation.
> 
> Many of the students we teach using Biolinux-X2GO-MATE quickly gain
> confidence and go on to install Biolinux on their own hardware.

Hi, Simon.

Glad to hear that :-)

Please will you post any Bio-Linux 8 bugs you know about to the list.

Thanks for your comments,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From tony.travis at minke-informatics.co.uk  Sat Apr 29 19:08:24 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Sun, 30 Apr 2017 00:08:24 +0100
Subject: [Bio-linux-list] Bio-Linux Unity Desktop
In-Reply-To: <195171347.7141959.1493409751299@mail.yahoo.com>
References: <f13b3138-88ba-ab61-ae67-5b401948508b@minke-informatics.co.uk>
	<VI1PR04MB1389F50CBCDC4161140843ADAE130@VI1PR04MB1389.eurprd04.prod.outlook.com>
	<195171347.7141959.1493409751299@mail.yahoo.com>
Message-ID: <ac114f40-d83c-4977-25ea-833e95a3dc14@minke-informatics.co.uk>

On 28/04/17 21:02, Brian Cady wrote:
> I vote for MATE, with it's better compatibility with older machines.

Hi, Brian.

I think this is important too.

Thanks for your comments,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk