[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)

[Tim Booth]

Hi Mike,
> 
> 1. When I initially ran the script I hit a question about whether or
> not to update a Grub config file.  There were about 7 or 8 different
> choices here, so I went conservative and chose to keep the version I
> have.  In hindsight should I have selected differently?  If so, how
> can I change this now?

The thing with Grub is it either makes your computer boot up or it
doesn't, so if it works it's right.  I think I configured Grub to say
"Bio-Linux" instead of "Ubuntu" in the menu which is pretty
inconsequential - the menu doesn't even appear on non-dual-boot
machines.

But if you really want to go round again again I think you can just do:

sudo apt-get install --reinstall grub

> 2. After the first run through of the script I had a fully operative
> Precise, but very little of BioLinux.  

That's right

> Repeat running of the script installed some additional things, but got
> to a point where there were still bits missing (QIIME hadn't updated
> fully - though it would run the QIIME shell no commands would work as
> it complained about the wrong version of numpy).  Running it several
> more times just gave the same result (T-coffee was in a loop, being
> marked for upgrade, but then never upgrading for example). I fixed
> this by updating via synaptic, which leaves me with a working QIIME.  

But this is unexpected.  The idea is that the script gets you to do a
full upgrade of all the existing stuff, then the second time round it
makes sure all the bioinformatics stuff is in place.  It sounds like
part one didn't fully complete, and you sensibly pushed it through using
Synaptic.

> I don't have the BioLinux background, so I suspect that I still have a
> partial install.  Is there a way to compare what should be installed
> and what I actually have?

The script does this internally, and is designed so that running it on a
fully upgraded system has essentially no effect.  Would you mind running
it again and sending me the full log (to me, not to the -dev list)?  You
can capture the output with 'tee':

sudo bash bl_do_update_to7.sh | tee ~/update_log.txt

You can also run just the bit that checks the package list and get it to 
report, so this is the direct answer to your question above.  Download
http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh and
run it using bash but *without* sudo.  What does it say?

> NX also not yet working (users attempting to access get a message
> saying 'access disabled by host').  Attempted to follow Tony's
> suggestions above - installed Fallback (which hadn't been installed),
> installed ubuntu-desktop (or so  thought) and purged network-manager,
> breaking my internet connection.  This fool suggests the update isn't
> quite fool-proof yet - I should be a professional caving canary ;)

This could be problematic if you depend heavily on NX, as Tony has
reported NX is not entirely happy.  If your machine just has a fixed
wired connection then the loss of network manager is not a problem as
you can set the network up the old fashioned way.  And in fact for a
server/workstation that doesn't move this is more sensible.  In the most
basic case you just add these lines to /etc/network.interfaces:

auto eth0
iface eth0 inet dhcp

This assumes your network card is called 'eth0'.  If not, use 'ifconfig
-a' to list available cards.  It also assumes you use DHCP.  If not, see
'man interfaces' for the syntax to set the address manually.

> Also I left my keys at home, which means my laptop is locked in a
> drawer. I'm fairly sure you can't help with this, but a lend of a
> jemmy would be useful. Today is fired.  

The bottom of the drawer is normally the best point of attack.  Even a
sturdy screwdriver might be enough on a cheaper desk.

> Any reccommendations?  Everything is backed up in case a full install
> is required - but we have a lot of users, so that would be a pain. 

Fix the network as above and keep at it for now, I'd say.  Do you have
users who need NX access right away or do you have leeway to try
tinkering with it as per Tony's suggestions?

Cheers,

TIM

ps. Thanks for the BL citation in your recent paper.  Dawn spotted it
via Google scholar alerts.

-- 
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
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