From tony.travis at minke-informatics.co.uk  Thu Aug  9 07:16:45 2018
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 9 Aug 2018 13:16:45 +0200
Subject: [Bio-linux-list] QIIME uinder Bio/Linux
In-Reply-To: <MM1P123MB0876C28A06568D3CE562BF04E5270@MM1P123MB0876.GBRP123.PROD.OUTLOOK.COM>
References: <bc10ebb6bbb4e4d7068766332f9d016a@environmentalomics.org>
	<MM1P123MB0876C28A06568D3CE562BF04E5270@MM1P123MB0876.GBRP123.PROD.OUTLOOK.COM>
Message-ID: <7f5540f5-8927-fa93-e55e-a2df17b94d38@minke-informatics.co.uk>

On 07/08/18 11:44, Timms-Wilson, Tracey wrote:
> 
> 
>> -----Original Message-----
>> From: Prof John Craf [mailto:j.a.craft at gcu.ac.uk]
>> Sent: 02 August 2018 11:20
>> 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 : Prof John Craft
>> Email : j.a.craft at gcu.ac.uk
>> Message : Is anyone at BioLinux using QIIME2. The original QIIME was bundled
>> with BioLinux so I am hopeful you are looking into updating and someone can
>> give me a guiding hand.

Hi, John.

Tracey forwarded your message to me and I'm CC'ing my reply to the
Bio-Linux list in case anyone else has the same question.

I recommend installing "Bioconda" under Bio-Linux 8:

> https://bioconda.github.io/

I use "Bioconda" to install QIIME, because QIIME is quite sensitive to
which versions of supporting software are used. The versions of QIIME
supported by "Bioconda" are 1.8.0, 1.9.1

> https://bioconda.github.io/recipes/qiime/README.html

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 Aug  9 07:22:31 2018
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 9 Aug 2018 13:22:31 +0200
Subject: [Bio-linux-list] Mailing list problems
Message-ID: <f0742afa-95c6-711b-6968-3b18779b1cc6@minke-informatics.co.uk>

Hi,

There were some problems with the bio-linux-list that are now fixed.

If you tried to post a message and it failed, please try again.

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 Aug 14 06:11:54 2018
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 14 Aug 2018 12:11:54 +0200
Subject: [Bio-linux-list] Bio-Linux 9
In-Reply-To: <DB6PR0401MB253450FF7697CE6F69DA6436AE390@DB6PR0401MB2534.eurprd04.prod.outlook.com>
References: <017989ab-5773-2599-f897-2aecd9ce9cf3@gmail.com>
	<DB6PR0401MB253450FF7697CE6F69DA6436AE390@DB6PR0401MB2534.eurprd04.prod.outlook.com>
Message-ID: <49e25926-8546-bfc0-25e6-0801fae8d07e@minke-informatics.co.uk>

On 13/08/18 14:31, Simon Wagstaff wrote:
> Hi Will,
> This is great news.
> 
> Very much appreciate the effort you and Tony continue to put into the project.
> 
> If I can help in any way please let me know.

Hi, Simon.

Thanks very much for your interest in Bio-Linux and your offer to help.

At present, Will is creating a meta-package for "bio-linux-desktop" with
help from Andreas Tille and the Debian-Med team. Our plan is to migrate
ALL the upstream bioinformatics packages present in Bio-Linux 8 to the
versions packaged and maintained by the Debian-Med team and drop all the
obsolete NERC/NERC repositories because we don't have access to them
since Tim Booth left the project. In any case, We have worked with the
Debian-Med team for many years. I attended the Debian-Med 'Sprint' in
Barcelona in February, where I put forward plans for Bio-Linux 9 to be
based on Ubuntu-MATE 18.04 + a subset of .deb packages from "med-bio":

> https://wiki.debian.org/Sprints/2018/DebianMed2018
Please join the Debian-Med team if you want to help:

> https://wiki.debian.org/DebianMed

I've CC'ed your message to the Bio-Linux mailing and Debian-Med lists in
case anyone else wants to help create the "bio-linux-desktop" and
"bio-linux-server" metapackages. So far, we've successfully remastered
the Ubuntu-MATE iso with packages from Debian-Med using "customiser":

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

However, we've not yet managed to enable 'persistence' on a 'live' USB.

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 Aug 16 06:47:21 2018
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 16 Aug 2018 12:47:21 +0200
Subject: [Bio-linux-list] Bio-Linux
In-Reply-To: <20180816062429.2ngm3s53z3clkmj3@an3as.eu>
References: <20180727231811.5r4fkkcd3ltw3r4z@an3as.eu>
	<e5f3c8f0-f51c-9d8a-9517-2f70f6c4e7e0@gmail.com>
	<9b86252b-3199-3187-3f1e-7ff7a2739cc6@minke-informatics.co.uk>
	<3be93d8b-06da-0a54-9fa7-d815bcb0a1d1@gmail.com>
	<20180806091207.ounvziynfmycjck2@an3as.eu>
	<9403a8e9-baa9-4cef-d2e1-aa405a4b9a62@gmx.de>
	<20180816062429.2ngm3s53z3clkmj3@an3as.eu>
Message-ID: <b418e2cc-1e9e-eec6-be57-55b1774da93b@minke-informatics.co.uk>

On 16/08/18 08:24, Andreas Tille wrote:
> [...]
> It would be a really helpful contribution from BioLinux if you could
> maintain this list to point package maintainers to the **urgently**
> **needed** software to start with this to spent our time in a sensible
> manner.  I'm also offering mentoring to learn how to properly package
> inside the Debian Med team[1].
>  
>> The https://blends.debian.org/med/tasks/bio pages have that yellow
>> section that lists a few bio-linux ones. How would you (Andreas and
>> Tony) feel about moving them to the Bio-Linux list?

Hi, Steffen and Andreas.

Good idea - I'll do that, but I'm on holiday just now driving through
France and only have intermittent access to the Internet. I'll do what I
can when I can. I won't be back home again until 2 Oct, but Will might
be able to sort it out for me.

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  Mon Aug 20 05:42:27 2018
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Mon, 20 Aug 2018 11:42:27 +0200
Subject: [Bio-linux-list] FW: biolinux
In-Reply-To: <AM6PR01MB4069DB9488EA523A8679F56DF5320@AM6PR01MB4069.eurprd01.prod.exchangelabs.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>
Message-ID: <5b58a09e-f0eb-b109-2e95-a08b0012f4f1@minke-informatics.co.uk>

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