[Bio-linux-dev] UEFI install, and bug in upgrade script

[Tim Booth]

Hi Tony,

Thanks for spotting the typo in the script - I'm not sure when that
crept in but rogue i's are one downside of being a Vim user.  It's
fixed.

I've made a new image recently (7.0.7) that I believe has all the latest
-lts-quantal compatibility packages present and correct.  I've just
announced that on the users list.

I don't know if this will address the UEFI issues as I have no UEFI test
machine but it seems from your reports like Casper+UEFI is still a
little flakey in any case.

If you want me to rebuild the Bio-Linux ISO from scratch starting with
the 12.04.2 release then I'd strongly suggest not holding your breath
waiting for that to happen.

Cheers,

TIM

On Mon, 2013-07-22 at 15:29 +0100, Tony Travis wrote:
> Hi, Tim.
> 
> You need to update Bio-Linux 7 to use Ubuntu 12.04.2 LTS for UEFI
> installs: The 12.04.1 LTS iso can not be used to install on a modern
> UEFI system e.g. the HP Probook 4440s that my colleague Mahendra has.
> 
> We installed 64-bit Ubuntu 12.04.2 LTS using a USB-stick created from
> the Ubuntu iso, but found that we _also_ had to have a CDROM in the
> drive to get it to run - Ubuntu keeps looking for a casper FS on
> /dev/sr0, even though it was booted from USB. I don't think this will
> happen if there is no CD drive present. Unfortunately, it would not boot
> off the CD(!). Anyway, we've got Ubuntu installed, and are now upgrading
> it to Bio-Linux using your script.
> 
> There is a show-stopper bug in your "bl_master_package_list.sh":
> 
> --- bl_master_package_list.sh.orig	2013-07-22 12:51:56.000000000 +0100
> +++ bl_master_package_list.sh	2013-07-22 15:20:28.145259890 +0100
> @@ -17,7 +17,7 @@
> 
>  if [ `id -u` = 0 ] ; then
>      echo "Running as root - will install for real."
> -    iinst="apt-get install -y "
> +    inst="apt-get install -y "
>  else
>      echo "Not running as root - will just print commands."
>      inst="echo sudo apt-get install"
> 
> Fixed, and installing now by running it manually.
> 
> HTH,
> 
>   Tony.

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

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

http://nebc.nerc.ac.uk
+44 1491 69 2705