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

[Tony Travis]

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.
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