updated cloudbiolinux ? in AWS

[Linda Molla]

Has cloud bio linux actually been updated in the last 5 years?

Which is the most recent updated AMI ?

[Brad Chapman]

Linda;
With CloudBioLinux we've moved away from providing a pre-built AMI and instead
providing components for easily installing tools yourself. Much of this work
has moved into the bioconda project if you're looking for tools:

https://bioconda.github.io/

If you'd like a pre-built set of tools for NGS that work together you might
want to look at bcbio:

http://bcb.io/

Sorry to not have exactly what you're looking for but hope this helps with
getting started,
Brad

> Has cloud bio linux actually been updated in the last 5 years?
> Which is the most recent updated AMI ?
>

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[Tony Travis]

On 01/11/17 15:56, Linda Molla wrote:
> Has cloud bio linux actually been updated in the last 5 years?
> Which is the most recent updated AMI ?

Hi,

I can't speak for Cloud-Bio-Linux, but I've created a public AMI for
NERC/EOS Bio-Linux 8 based on the .ova file created by Tim Booth:

ami-2dee1954

We've also updated the .iso image to Bio-Linux 8.0.8:

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

Release notes:

The Bio-Linux 8.0.8 point release contains an updated Linux kernel to
improve support for modern WiFi chipsets in particular and all the
packages have been updated. This release is mainly intended to improve
the use of Bio-Linux on a USB-stick or DVD. However, the 8.0.8 release
also has "mdadm" pre-installed to make installation and rescue of
Bio-Linux instances on "md" RAID simpler.

PLEASE NOTE: Bio-Linux 8.0.7 instances installed to hard disk do NOT
need to be updated using the Bio-Linux 8.0.8 point release. Bio-Linux is
normally configured for unattended upgrades of core packages and will be
upgraded automatically in situ. A manual update will be necessary to
upgrade ALL packages installed:

sudo apt update
sudo apt full-upgrade

Changelog:

The Bio-Linux 8.0.8 point release was created using Tim Booth's
"build-bio-linux" scripts updated and modified by Will McCaffery and
Tony Travis:

https://github.com/Bio-Linux/

HTH,

Tony.

[Tony Travis]

On 01/11/17 16:15, Brad Chapman wrote:
>
> Linda;
> With CloudBioLinux we've moved away from providing a pre-built AMI and instead
> providing components for easily installing tools yourself. Much of this work
> has moved into the bioconda project if you're looking for tools:
>
> https://bioconda.github.io/

Hi, Brad.

I've taken over from Tim Booth as the Bio-Linux lead developer and will
continue to make steady progress towards Bio-Linux 9. I'm already using
"bioconda" for QIIME" under Bio-Linux 8 and would like to use it more in
Bio-Linux 9. However, I still think there is a good use-case for a
'live' distribution that you can run from a USB-stick or DVD, or install
onto a laptop/desktop/server without having to download and configure a
lot of software yourself. IMHO, CLC is not the answer!

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....@minke-informatics.co.uk

[Brad Chapman]

Tony;
This is awesome news, I'm so happy you're continuing to build Bio-Linux. To be
clear, it's not that I don't think pre-built images are useful, it's more that
we haven't had resources to support them so try for the next best thing with
the bcbio distribution and bioconda for configuration. I'm glad you're
continuing to work on this,
Brad

> I've taken over from Tim Booth as the Bio-Linux lead developer and will
> continue to make steady progress towards Bio-Linux 9. I'm already using
> "bioconda" for QIIME" under Bio-Linux 8 and would like to use it more in
> Bio-Linux 9. However, I still think there is a good use-case for a
> 'live' distribution that you can run from a USB-stick or DVD, or install
> onto a laptop/desktop/server without having to download and configure a
> lot of software yourself. IMHO, CLC is not the answer!
>
> 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....@minke-informatics.co.uk
>

[CARLOS LIZAMA]

Hi brad,

Do you know if has any community ami in amazon aws or other cloud with the tools for NS analysis?

thanks

carlos

[Tony Travis]

On 14/11/17 23:40, CARLOS LIZAMA wrote:
> Hi brad,
>
> Do you know if has any community ami in amazon aws or other cloud with
> the tools for NS analysis?

Hi, Carlos.

I've created a public AMI for Bio-Linux 8, based on Tim Booth's .ova:

Name: Bio-Linux 8.0.7
AMI Name: import-ami-fgi1q789
AMI ID: ami-2dee1954

HTH,

[Enis Afgan]

Hi Carlos, 

There is also the Genomics Virtual Lab (GVL) platform available on AWS with a variety of tools available. More info available https://www.gvl.org.au/ and an instance can be launched via this portal https://beta.launch.usegalaxy.org/catalog/appliance/genomics-virtual-lab

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