[Bio-Linux] Bio-Linux 8.0.7

[Ian Donaldson]

The updates sound very helpful.  Has there been any update to the version of Galaxy?

Thanks,
Ian

________________________________________
From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
Sent: 17 June 2015 17:30
To: bio-linux at nebclists.nerc.ac.uk
Subject: [Bio-Linux] Bio-Linux 8.0.7

Dear Bio-Linux users,

I've just put out a point release of Bio-Linux 8.  As usual, existing
users of installed systems do not need to do anything to get automatic
package updates but there are a couple of things that might be of
interest if you especially if you are running Bio-Linux as a VM (see 5
and 6).

1)
I've set it so machines installed from this image will install security
patches and basic updates silently and without prompting.  At the moment
you are automatically notified but you have to approve the installation.

If you want to enable this on your existing machine grab this script:
http://nebc.nerc.ac.uk/downloads/bl8_only/unattended_upgrade.sh
and run it as root:
$ sudo bash unattended_upgrade.sh

Note that this only applies to security updates and updates that don't
change package dependencies.  For other updates you'll still be prompted
to confirm.

2)
The OSwitch package for Docker is installed by default, but you still
need to add Docker to the system to run it.  A Docker set-up script is
provided under /usr/share/oswitch/contrib/docker_setup_ubuntu.sh
See https://github.com/wurmlab/oswitch

I've also added the Stacks package which was previously mentioned on
this list:
http://catchenlab.life.illinois.edu/stacks/

3)
MySQL is no longer on the default image.  Most people don't use it, and
for those who do need it the server can be added back very easily
(apt-get install mysql-server).  Note that Ubuntu also supports
mariadb-server 5.5 if you prefer to use that instead.

4)
I've removed a bunch of redundant 32-bit libs, saving some space and
fixing a dependency conflict issue.  The update manager should also
purge these libraries from existing systems for you.

5)
VirtualBox now uses the "Paravirtualized" network device by default.
This is much faster for downloads onto the VM and is recommended for all
users.  Shut down your VM then look under Network -> Adapter1 ->
Advanced -> Adapter Type and simply change it to the last option before
booting back up again.

6)
I've increased the HD size on the VirtulBox image to a more useful
100GB.  Under VirtualBox this will only use extra disk space on your
host system if you actually put stuff on the disk, but for other VM
systems it may use up space right away.  There remains no satisfactory
way to increase the main disk size for your existing VMs - you generally
need to add on and format an extra disk as discussed previously on this
list.

And that's it.  Enjoy!

TIM

--
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://environmentalomics.org/bio-linux
+44 1491 69 2297


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