[Bio-Linux] Bio-Linux 8.0.7

Thu Jun 18 07:14:25 EDT 2015

Hi Ian,

The problem here is that it would immediately take up 100GB on every
users machine, which is a bit scary.  Also my impression is that while
writes are slow while the disk is expanding, overwriting and reading are
still fast.

It's reasonably easy to make the switch yourself.  Use the "Virtual
Media Manager" to copy the disk as a fixed-size VDI, then under machine
settings unplug the VMDK disk and connect the new VDI version.

Actually, I think it might even be the case that when you export the
machine as an OVA the disk automatically reverts to a dynamically-sized
VMDK.  I think this might be a feature of the .OVA spec - to be honest I
never tried it.

Cheers,

TIM

> BTW would it be possible to create a version of the BL-VM as a static
> drive size, rather than dynamic one?  I am under the impression that
> read/write access is much slower using a dynamic sized VM.
> 
> Ian
> 
> ________________________________________
> From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
> Sent: 18 June 2015 10:07
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Bio-Linux 8.0.7
> 
> Hi Ian,
> 
> Sadly not.  It's just too big a job since they changed the way the
> configuration works.  I have to construct a package that will switch
> from the old system to the new one without breaking the configuration or
> losing any data.  It's on my TODO list but it's likely to be near the
> end of the year before I have tome to tackle it.  The Galaxy developers
> make encouraging noises about wanting to support a package but when I
> look for actual help with the work I have no luck.  I think they are
> more focussed on having Galaxy as a complete self-contained server
> system than something that integrates with other packages on Bio-Linux,
> which I guess makes sense from their point of view, but it makes things
> hard for me.
> 
> Cheers,
> 
> TIM
> 
> On Thu, 2015-06-18 at 08:40 +0000, Ian Donaldson wrote:
> > 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
> >
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> --
> 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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-- 
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