From tony.travis at minke-informatics.co.uk  Sat Sep 22 10:37:21 2018
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Sat, 22 Sep 2018 16:37:21 +0200
Subject: [Bio-linux-list] Bio-Linux 8.0.8 on Amazon EC2
Message-ID: <43192aef-815c-b706-5012-70a4aa4b0dd8@minke-informatics.co.uk>

Hi,

I've updated my public Bio-Linux AMI (Amazon Machine Image) on EC2:

  https://aws.amazon.com/

Search Public images for:

  Bio-Linux 8.0.8 (ami-0099438a280b1df20)

This is an updated AMI based on the NEBC/EOS Bio-Linux 8.0.7 OVA:

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

[Log in as manager with initial password manager and reset the password]

It needs to be launched as an EC2 VM type of at least "t2.medium" to be
useful, but it can be launched with an EC2 VM type of "t2.micro" that is
more limited, but "t2.micro" is eligible for the AWS EC2 'free' tier.

Let me know if you try it out,

  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 Simon.Wagstaff at lstmed.ac.uk  Wed Sep 26 07:48:16 2018
From: Simon.Wagstaff at lstmed.ac.uk (Simon Wagstaff)
Date: Wed, 26 Sep 2018 11:48:16 +0000
Subject: [Bio-linux-list] FW: biolinux
In-Reply-To: <5b58a09e-f0eb-b109-2e95-a08b0012f4f1@minke-informatics.co.uk>
References: <HE1PR0102MB3113543972B875008EF91960F5B30@HE1PR0102MB3113.eurprd01.prod.exchangelabs.com>
	<VI1PR06MB1711555A9413A3A15D403216E5B00@VI1PR06MB1711.eurprd06.prod.outlook.com>
	<71c9a275-2394-f884-4fb9-98a791a524f8@minke-informatics.co.uk>
	<HE1PR0102MB31138C43DC271809B3160280F5B00@HE1PR0102MB3113.eurprd01.prod.exchangelabs.com>
	<6b97fd28-b360-417f-90e3-2a8fddfc7f1e@minke-informatics.co.uk>
	<AM6PR01MB4069DB9488EA523A8679F56DF5320@AM6PR01MB4069.eurprd01.prod.exchangelabs.com>
	<5b58a09e-f0eb-b109-2e95-a08b0012f4f1@minke-informatics.co.uk>
Message-ID: <DB6PR0401MB2534F5D72468806956B53661AE150@DB6PR0401MB2534.eurprd04.prod.outlook.com>

Hi Tony,
We have an increasing number of people working with Galaxy on Biolinux 8. I understand that previous upgrades of Ubuntu break the BL version of Galaxy but I was wondering if there are plans to include Galaxy in the Bio-Linux 9 project?

Thanks,

Simon

-----Original Message-----
From: Bio-Linux-list [mailto:bio-linux-list-bounces at bioinformatics.org] On Behalf Of Tony Travis
Sent: 20 August 2018 10:42
To: Stefan WECKX <Stefan.Weckx at vub.be>
Cc: Bio-Linux mailing list <bio-linux-list at bioinformatics.org>; Debian Med Project List <debian-med at lists.debian.org>
Subject: Re: [Bio-linux-list] FW: biolinux

On 20/08/18 08:59, Stefan WECKX wrote:
> Hi Tony,
>
>
>
> Any update on the expected release date?

Hi, Stefan.

Sorry, I'm away on holiday in the French Pyranees just now, with only intermittent access to my email. I'll be working in Milan afterwards until 2 Oct before I look at the Bio-Linux 9 project seriously again.

I attended a Debian-Med Sprint in Barcelona in Feb where I gave a short presentation about my proposal to base Bio-Linux 9 on Ubuntu-MATE 18.04 LTS + Debian-Med with help from the Debian-Med team:

> https://wiki.debian.org/Sprints/2018/DebianMed2018

Will McAffery has been working hard to create a "bio-linux-desktop'
meta-package over the summer with help from the Debian-Med team and we've remastered the Ubuntu-MATE 18.04 LTS iso adding packages from Debian-Med's 'med-bio' task using "customizer":

> https://github.com/kamilion/customizer

At present, we've not yet been able to create a 'live' USB-stick with persistence, but we've tested using the 'live' stick without persistence and used it to install to single and "md" RAID hard disks successfully.

I can't give you a precise date for the release, but meanwhile it would be very useful if you and anyone else interested could let us know which packages from Bio-Linux 8 are the most useful/important to you?

The Debian-Med team have offered to help package any software that is included in Bio-Linux 8, but not available in Debian "Sid", which is what Ubuntu is based on.

I've CC'ed my reply to the Bio-Linux and Debian-Med mailing lists to keep everyone up-to-date with the current state of Bio-Linux 9.

Bye,

  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
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From tony.travis at minke-informatics.co.uk  Wed Sep 26 08:57:55 2018
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Wed, 26 Sep 2018 14:57:55 +0200
Subject: [Bio-linux-list] FW: biolinux
In-Reply-To: <DB6PR0401MB2534F5D72468806956B53661AE150@DB6PR0401MB2534.eurprd04.prod.outlook.com>
References: <HE1PR0102MB3113543972B875008EF91960F5B30@HE1PR0102MB3113.eurprd01.prod.exchangelabs.com>
	<VI1PR06MB1711555A9413A3A15D403216E5B00@VI1PR06MB1711.eurprd06.prod.outlook.com>
	<71c9a275-2394-f884-4fb9-98a791a524f8@minke-informatics.co.uk>
	<HE1PR0102MB31138C43DC271809B3160280F5B00@HE1PR0102MB3113.eurprd01.prod.exchangelabs.com>
	<6b97fd28-b360-417f-90e3-2a8fddfc7f1e@minke-informatics.co.uk>
	<AM6PR01MB4069DB9488EA523A8679F56DF5320@AM6PR01MB4069.eurprd01.prod.exchangelabs.com>
	<5b58a09e-f0eb-b109-2e95-a08b0012f4f1@minke-informatics.co.uk>
	<DB6PR0401MB2534F5D72468806956B53661AE150@DB6PR0401MB2534.eurprd04.prod.outlook.com>
Message-ID: <82226796-6ca8-7cb7-4799-da7fe4913a62@minke-informatics.co.uk>

On 26/09/18 13:48, Simon Wagstaff wrote:
> Hi Tony,
> We have an increasing number of people working with Galaxy on Biolinux 8. I understand that previous upgrades of Ubuntu break the BL version of Galaxy but I was wondering if there are plans to include Galaxy in the Bio-Linux 9 project?

Hi, Simon.

With help from the Debian-Med team, we are creating two metapackages:

  bio-linux-desktop
  bio-linux-server

Galaxy will be included in the server meta-package, but not in the
desktop package. My plan is that these meta-packages will eventually
arrive in the standard Ubuntu repositories via Debian Sid, which Ubuntu
is based on, and can be added to an existing Ubuntu 18.04 instance.

The Bio-Linux 9 USB-stick will be based on the desktop meta-package, so
that typical low-spec. laptops can use it without having to run server
processes by default.

Please join us in the Debian-Med team, and encourage others to, if you
want to help shape the future direction of Bio-Linux:

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

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