From tbooth at ceh.ac.uk  Mon Oct  1 09:14:49 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 1 Oct 2012 14:14:49 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk>	<5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur>	<50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
Message-ID: <1349097289.24717.1.camel@balisaur>

Hi,

Many thanks for trying the script and for all the feedback.

> Since you said "should also be fine if run on a vanilla Ubuntu 12.04
> box (or even on regular Ubuntu 10.04)" I decided to give a try for the
> new version of Ubuntu Studio 12.04 64 bits that comes with Xfce and
> all the cool stuff for Audio ,Graphics ,Video , Photography and
> Publishing already installed.
> 
> So far no regrets, the panels and menus are looking very similar with
> the old gnome 2 style, very nice look and feel and I loved the very
> minimalistic button on the top left that give you access to everything
> you need inside a single menu. (Also with the bioinformatics submenu)

> Of course you can always install Unity if you think this will improve
> your productivity. (not my case) :P
> 
Good to know that everything installs onto Ubuntu Studio and the menus
look OK.  I've not used this distro myself but from a quick look it
seems to be in the same area as Linux Mint but without the nasty green
interface, which can't be bad.

> Before trying this I upgraded my old version of Biolinux 6 and this
> gave me the feeeling that I just got a brand new Ubuntu 12.04/Unity
> without anything special or specific for Bioinformatics. 

> I know the packages were installled but the feeling was not the same. 
> (I hope/imagine you guys will make a good artwork before the official 
> release to make it looks more like Biolinux, am I right ?)

Yes, the custom wallpaper is literally the only branding on there now,
but I intend to add some more and to try and make the bioinformatics
tools more prominent as discussed before.

> Another thing I would like to suggest is a categorization of all the
> apps installed related with Bioinformatics. Ubuntu Studio once again,
> did a really good job splitting into Audio, Photography, Graphics and
> Video. Would be nice to have something like that for Biolinux, ex:
> DNA, RNA, Protein, NGS ... and so on ... just a suggestion.

We already have some of that info buried in the documentation pages, so
I've been considering how best to expose that within Unity.  Maybe by
adding it to the appropriate .desktop files or by adding a custom lens,
which may be easier than I first thought using Singlet
(http://mhall119.com/2012/01/simplified-unity-lens-development-with-singlet/).

> One of the things would be really nice to have in Biolinux is a meta
> package Same way Ubuntu Studio has, so everyone could convert his
> Ubuntu based distro in Biolinux.
> https://launchpad.net/ubuntu/+source/ubuntustudio-meta
> https://help.ubuntu.com/community/Ubuntu%20Studio%20Upgrade%20from%
> 20Ubuntu

Indeed, and I could convert the update script (or at least a portion of
it) into a package with a big set of dependencies.  But at this stage
it's easier just to have a script.  My priority is to give existing
Bio-Linux users a one-shot upgrade, but the fact that this also works on
Vanilla Ubuntu/Ubuntu Studio is a bonus.

Cheers,

TIM


> On Thu, Sep 27, 2012 at 1:50 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>         Hi Dan,
>         
>         I'm looking into how best to customise the default panel on
>         the Unity
>         Dash.  The things that come up when you click the Ubuntu logo
>         at the top
>         (AKA the BFB - big freakin button) are called 'lenses' - the
>         Home lens,
>         the Applications lens, the Files lens etc. I looked at what it
>         would
>         take to make my own bioinformatics lens - there are full
>         instructions -
>         and it might be worth a shot but then it might take weeks to
>         perfect and
>         I'd like a quicker solution.
>         
>         The Home lens with the smart search is pretty neat, but some
>         of the
>         others aren't even very good for Ubuntu, never mind
>         Bio-Linux.  How the
>         heck is it generating "Apps available for Download" in the
>         Applications
>         lens?  It seems to pick some totally random packages, then, if
>         you click
>         one, next time you look it generates another random
>         selection.  How
>         pointless!
>         
>         I agree that having a folder of app links and putting Galaxy
>         in the side
>         bar is probably the quickest way to get something acceptable,
>         though
>         it's not ideal.
>         >
>         Cheers,
>         
>         TIM
>         
>         > Do you plan to change around the unity hotlinks for the
>         final distro?
>         > I imagine a folder of links to bioinformatics programs would
>         be useful
>         > to new users, and unity is a bit annoying in the
>         > no hierarchical menus. Maybe as Galaxy is the flagship, pin
>         that to
>         > the main menu, and drop ubuntuone etc
>         >
>         >
>         > Dan
>         >
>         >
>         > On 27 September 2012 12:03, Tim Booth <tbooth at ceh.ac.uk>
>         wrote:
>         >         Hi Dan,
>         >
>         >         On Thu, 2012-09-27 at 11:51 +0100, Daniel Pass
>         wrote:
>         >         > Currently I have only gone the route of
>         Ubuntu12.04 into BL7
>         >         on my
>         >         > laptop, but that seemed to work flawlessly
>         although did need
>         >         a couple
>         >         > of re-runs. Qiime continues to work as before.
>         >         >
>         >
>         >         So you can confirm you now have Qiime 1.5, right?
>         >         >
>         >         > Im running it on my virtual box now but keeping
>         expectations
>         >         low after
>         >         > you said there were issues with it before, Tim. It
>         won't let
>         >         me run
>         >         > the script straight, and keeps forcing the
>         'upgrade to
>         >         12.04' gui on
>         >         > me so letting it do that first so assuming it'll
>         go after
>         >         that.
>         >         >
>         >
>         >         The script can't do its work until the base system
>         is updated
>         >         to Ubuntu
>         >         12.04.  This brings with it things like the kernel,
>         Gnome,
>         >         python, etc.
>         >         This bit of the update is handled by the Ubuntu
>         upgrade GUI.
>         >
>         >         If you think you are already upgraded to 12.04 but
>         you still
>         >         get this
>         >         situation then let me know.
>         >
>         >         Cheers,
>         >
>         >         TIM
>         >         >
>         >
>         >         --
>         >         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
>         >         --
>         >         This message (and any attachments) is for the
>         recipient only.
>         >         NERC
>         >         is subject to the Freedom of Information Act 2000
>         and the
>         >         contents
>         >         of this email and any reply you make may be
>         disclosed by NERC
>         >         unless
>         >         it is exempt from release under the Act. Any
>         material supplied
>         >         to
>         >         NERC may be stored in an electronic records
>         management system.
>         >
>         >         _______________________________________________
>         >         Bio-Linux-dev mailing list
>         >         Bio-Linux-dev at nebclists.nerc.ac.uk
>         >
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>         >
>         >
>         >
>         >
>         >
>         > --
>         >
>         >
>         >
>         > Daniel Pass
>         >
>         > Tel: (029208)76680
>         > Mob: 07735658687
>         > http://www.kille-morgan.org.uk
>         >
>         > Room 0.39,
>         > School of Biosciences,
>         > Biological Sciences Building,
>         > Museum Avenue,
>         > Cardiff,
>         > CF10 3AT
>         >
>         >
>         >
>         
>         --
>         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
>         _______________________________________________
>         Bio-Linux-dev mailing list
>         Bio-Linux-dev at nebclists.nerc.ac.uk
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>         
> 

-- 
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



From gawbul at gmail.com  Mon Oct  1 16:35:56 2012
From: gawbul at gmail.com (Steve Moss)
Date: Mon, 1 Oct 2012 21:35:56 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
Message-ID: <CALKAsdpj_RTEOHjTo45YaFOuRtUiEjEfWdURfopBGQK4kFz6bw@mail.gmail.com>

Dear Tim,

I've just run through the upgrade process on an existing Ubuntu 12.04
release (on my laptop at home) and have had no problems at all. Everything
installed smoothly! Excellent script, thanks!

Will upgrade our bioinformatics lab PCs when I'm next in and let you know
how that goes :)

Cheers,

Steve

-- 
Kindest regards,

Steve Moss
http://about.me/gawbul <http://stevemoss.ath.cx>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20121001/411827ae/attachment.html>

From tbooth at ceh.ac.uk  Fri Oct  5 11:40:05 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 5 Oct 2012 16:40:05 +0100
Subject: [Bio-linux-dev] Something for the weekend - new Plymouth boot logo
Message-ID: <1349451605.3001.5.camel@balisaur>

Hi,

Still no bootable ISO for Bio-Linux 7 just yet, but if anyone on this
list has upgraded to BL7 and is irked to still see the Bio-Linux 6 logo
(or the Ubuntu logo depending on your setup) during boot-up then this is
for you:

apt-get install bio-linux-plymouth-theme

Note - if you didn't see a boot logo with progress dots under it at all
before then don't expect to see one now (Plymouth doesn't work on all
graphics cards and I'm not  the man to fix it - you're stuck with the
blank screen).  If you have other problems with the package - eg. still
seeing the old logo - then do let me know.

Cheers,

TIM

-- 
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
-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.

From mikeyj.cox at gmail.com  Thu Oct 11 04:29:22 2012
From: mikeyj.cox at gmail.com (Mike Cox)
Date: Thu, 11 Oct 2012 09:29:22 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <1349097289.24717.1.camel@balisaur>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
Message-ID: <CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>

Hi Tim,

Have just bitten the bullet and run the script on our BL6 box.  One or two
hiccups:

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?

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

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?

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 ;)

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.

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.

Cheers

Mike

blog: http://palecomic.tumblr.com/
skype: mikeyjcox
twitter: mikeyj


On Mon, Oct 1, 2012 at 2:14 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi,
>
> Many thanks for trying the script and for all the feedback.
>
> > Since you said "should also be fine if run on a vanilla Ubuntu 12.04
> > box (or even on regular Ubuntu 10.04)" I decided to give a try for the
> > new version of Ubuntu Studio 12.04 64 bits that comes with Xfce and
> > all the cool stuff for Audio ,Graphics ,Video , Photography and
> > Publishing already installed.
> >
> > So far no regrets, the panels and menus are looking very similar with
> > the old gnome 2 style, very nice look and feel and I loved the very
> > minimalistic button on the top left that give you access to everything
> > you need inside a single menu. (Also with the bioinformatics submenu)
>
> > Of course you can always install Unity if you think this will improve
> > your productivity. (not my case) :P
> >
> Good to know that everything installs onto Ubuntu Studio and the menus
> look OK.  I've not used this distro myself but from a quick look it
> seems to be in the same area as Linux Mint but without the nasty green
> interface, which can't be bad.
>
> > Before trying this I upgraded my old version of Biolinux 6 and this
> > gave me the feeeling that I just got a brand new Ubuntu 12.04/Unity
> > without anything special or specific for Bioinformatics.
>
> > I know the packages were installled but the feeling was not the same.
> > (I hope/imagine you guys will make a good artwork before the official
> > release to make it looks more like Biolinux, am I right ?)
>
> Yes, the custom wallpaper is literally the only branding on there now,
> but I intend to add some more and to try and make the bioinformatics
> tools more prominent as discussed before.
>
> > Another thing I would like to suggest is a categorization of all the
> > apps installed related with Bioinformatics. Ubuntu Studio once again,
> > did a really good job splitting into Audio, Photography, Graphics and
> > Video. Would be nice to have something like that for Biolinux, ex:
> > DNA, RNA, Protein, NGS ... and so on ... just a suggestion.
>
> We already have some of that info buried in the documentation pages, so
> I've been considering how best to expose that within Unity.  Maybe by
> adding it to the appropriate .desktop files or by adding a custom lens,
> which may be easier than I first thought using Singlet
> (
> http://mhall119.com/2012/01/simplified-unity-lens-development-with-singlet/
> ).
>
> > One of the things would be really nice to have in Biolinux is a meta
> > package Same way Ubuntu Studio has, so everyone could convert his
> > Ubuntu based distro in Biolinux.
> > https://launchpad.net/ubuntu/+source/ubuntustudio-meta
> > https://help.ubuntu.com/community/Ubuntu%20Studio%20Upgrade%20from%
> > 20Ubuntu
>
> Indeed, and I could convert the update script (or at least a portion of
> it) into a package with a big set of dependencies.  But at this stage
> it's easier just to have a script.  My priority is to give existing
> Bio-Linux users a one-shot upgrade, but the fact that this also works on
> Vanilla Ubuntu/Ubuntu Studio is a bonus.
>
> Cheers,
>
> TIM
>
>
> > On Thu, Sep 27, 2012 at 1:50 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> >         Hi Dan,
> >
> >         I'm looking into how best to customise the default panel on
> >         the Unity
> >         Dash.  The things that come up when you click the Ubuntu logo
> >         at the top
> >         (AKA the BFB - big freakin button) are called 'lenses' - the
> >         Home lens,
> >         the Applications lens, the Files lens etc. I looked at what it
> >         would
> >         take to make my own bioinformatics lens - there are full
> >         instructions -
> >         and it might be worth a shot but then it might take weeks to
> >         perfect and
> >         I'd like a quicker solution.
> >
> >         The Home lens with the smart search is pretty neat, but some
> >         of the
> >         others aren't even very good for Ubuntu, never mind
> >         Bio-Linux.  How the
> >         heck is it generating "Apps available for Download" in the
> >         Applications
> >         lens?  It seems to pick some totally random packages, then, if
> >         you click
> >         one, next time you look it generates another random
> >         selection.  How
> >         pointless!
> >
> >         I agree that having a folder of app links and putting Galaxy
> >         in the side
> >         bar is probably the quickest way to get something acceptable,
> >         though
> >         it's not ideal.
> >         >
> >         Cheers,
> >
> >         TIM
> >
> >         > Do you plan to change around the unity hotlinks for the
> >         final distro?
> >         > I imagine a folder of links to bioinformatics programs would
> >         be useful
> >         > to new users, and unity is a bit annoying in the
> >         > no hierarchical menus. Maybe as Galaxy is the flagship, pin
> >         that to
> >         > the main menu, and drop ubuntuone etc
> >         >
> >         >
> >         > Dan
> >         >
> >         >
> >         > On 27 September 2012 12:03, Tim Booth <tbooth at ceh.ac.uk>
> >         wrote:
> >         >         Hi Dan,
> >         >
> >         >         On Thu, 2012-09-27 at 11:51 +0100, Daniel Pass
> >         wrote:
> >         >         > Currently I have only gone the route of
> >         Ubuntu12.04 into BL7
> >         >         on my
> >         >         > laptop, but that seemed to work flawlessly
> >         although did need
> >         >         a couple
> >         >         > of re-runs. Qiime continues to work as before.
> >         >         >
> >         >
> >         >         So you can confirm you now have Qiime 1.5, right?
> >         >         >
> >         >         > Im running it on my virtual box now but keeping
> >         expectations
> >         >         low after
> >         >         > you said there were issues with it before, Tim. It
> >         won't let
> >         >         me run
> >         >         > the script straight, and keeps forcing the
> >         'upgrade to
> >         >         12.04' gui on
> >         >         > me so letting it do that first so assuming it'll
> >         go after
> >         >         that.
> >         >         >
> >         >
> >         >         The script can't do its work until the base system
> >         is updated
> >         >         to Ubuntu
> >         >         12.04.  This brings with it things like the kernel,
> >         Gnome,
> >         >         python, etc.
> >         >         This bit of the update is handled by the Ubuntu
> >         upgrade GUI.
> >         >
> >         >         If you think you are already upgraded to 12.04 but
> >         you still
> >         >         get this
> >         >         situation then let me know.
> >         >
> >         >         Cheers,
> >         >
> >         >         TIM
> >         >         >
> >         >
> >         >         --
> >         >         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
> >         >         --
> >         >         This message (and any attachments) is for the
> >         recipient only.
> >         >         NERC
> >         >         is subject to the Freedom of Information Act 2000
> >         and the
> >         >         contents
> >         >         of this email and any reply you make may be
> >         disclosed by NERC
> >         >         unless
> >         >         it is exempt from release under the Act. Any
> >         material supplied
> >         >         to
> >         >         NERC may be stored in an electronic records
> >         management system.
> >         >
> >         >         _______________________________________________
> >         >         Bio-Linux-dev mailing list
> >         >         Bio-Linux-dev at nebclists.nerc.ac.uk
> >         >
> >         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> >         >
> >         >
> >         >
> >         >
> >         >
> >         > --
> >         >
> >         >
> >         >
> >         > Daniel Pass
> >         >
> >         > Tel: (029208)76680
> >         > Mob: 07735658687
> >         > http://www.kille-morgan.org.uk
> >         >
> >         > Room 0.39,
> >         > School of Biosciences,
> >         > Biological Sciences Building,
> >         > Museum Avenue,
> >         > Cardiff,
> >         > CF10 3AT
> >         >
> >         >
> >         >
> >
> >         --
> >         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
> >         _______________________________________________
> >         Bio-Linux-dev mailing list
> >         Bio-Linux-dev at nebclists.nerc.ac.uk
> >         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> >
> >
>
> --
> 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
>
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20121011/d58c4e51/attachment.html>

From tony.travis at ed.ac.uk  Thu Oct 11 06:05:52 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Thu, 11 Oct 2012 11:05:52 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
Message-ID: <50769A00.5020500@ed.ac.uk>

On 11/10/12 09:29, Mike Cox wrote:
> [...]
> 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?

Hi, Mike.

I've got a simple script to compare what's installed on a system 
relative to the distribution manifest generated from an iso image or on 
two Debian/Ubuntu systems. I tried posting it to this list before, but 
it was blocked by the automatic moderation policy. Let me know if you 
want a copy and I'll email it to you directly.

> 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.

Was NX working before the upgrade?

Our NX is broken, because much of "ubuntu-desktop" consists of 
recommended packages that are not installed by default. In particular, 
there is no logout button on the Gnome fall-back desktop and only the 
system font is available and it renders very badly on the NX desktop. 
I'm working on these problems and will post an update about what I discover.

>  This fool suggests the update isn't quite
> fool-proof yet - I should be a professional caving canary ;)
> 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.

Personally, I think creating a Bio-Linux 7 terminal server would be 
quite useful. We're not quite there yet, but Tim's efforts have brought 
us within reach of that goal and *any* contribution you can make about 
using Bio-Linux in this way would be very useful. Bio-Linux is as much 
about building a community as it is about creating a Linux distribution.

> 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.

Check /var/log/auth.log to see what is happening when people try to 
connect via NX. Make sure nx and the users are permitted to login via 
SSH. Check the ~/.nx folder.

If you create a temporary account for me with sudo rights I'll login and 
check it out for you (please contact me at my company email if you want 
me to do this: tony.travis at minke-informatics.co.uk).

Bye,

   Tony.


From tbooth at ceh.ac.uk  Thu Oct 11 06:47:50 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 11 Oct 2012 11:47:50 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
Message-ID: <1349952470.2893.187.camel@balisaur>

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
-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.

From mikeyj.cox at gmail.com  Thu Oct 11 08:02:48 2012
From: mikeyj.cox at gmail.com (Cox, Michael J)
Date: Thu, 11 Oct 2012 13:02:48 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <50769A00.5020500@ed.ac.uk>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
Message-ID: <92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>

Thanks Tony, Thanks Tim

Internet restored.  Ran the update script and the package list script and will forward both to you Tim, the list of things not installed is quite long - includes galaxy, raxml and a number of r-cran packages.  

We can get around NX for the moment, I'll get people using putty or winSCP in the meantime, but it's really helpful for a number of the users that are used to desktop environments.  After sorting the network connection, NX now working, but it seems much slower than it was and various bits of the desktop are missing, sidebar the most noticeable.  

Users definitely have ssh permissions as per http://nebc.nerc.ac.uk/tools/bio-linux/accessing-bio-linux - interesting list of stuff after recent NX login in auth.log one of which seems to be related to a constant keychain message and the screen-saver lock, which doesn't clear with entering the user's password.  

No problem with citation Tim - very welcome!  Will contact with files off list.

Thanks again for your help

Mike






On 11 Oct 2012, at 11:05, Tony Travis <tony.travis at ed.ac.uk> wrote:

> On 11/10/12 09:29, Mike Cox wrote:
>> [...]
>> 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?
> 
> Hi, Mike.
> 
> I've got a simple script to compare what's installed on a system relative to the distribution manifest generated from an iso image or on two Debian/Ubuntu systems. I tried posting it to this list before, but it was blocked by the automatic moderation policy. Let me know if you want a copy and I'll email it to you directly.
> 
>> 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.
> 
> Was NX working before the upgrade?
> 
> Our NX is broken, because much of "ubuntu-desktop" consists of recommended packages that are not installed by default. In particular, there is no logout button on the Gnome fall-back desktop and only the system font is available and it renders very badly on the NX desktop. I'm working on these problems and will post an update about what I discover.
> 
>> This fool suggests the update isn't quite
>> fool-proof yet - I should be a professional caving canary ;)
>> 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.
> 
> Personally, I think creating a Bio-Linux 7 terminal server would be quite useful. We're not quite there yet, but Tim's efforts have brought us within reach of that goal and *any* contribution you can make about using Bio-Linux in this way would be very useful. Bio-Linux is as much about building a community as it is about creating a Linux distribution.
> 
>> 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.
> 
> Check /var/log/auth.log to see what is happening when people try to connect via NX. Make sure nx and the users are permitted to login via SSH. Check the ~/.nx folder.
> 
> If you create a temporary account for me with sudo rights I'll login and check it out for you (please contact me at my company email if you want me to do this: tony.travis at minke-informatics.co.uk).
> 
> Bye,
> 
>  Tony.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20121011/4be83d2b/attachment.html>

From tbooth at ceh.ac.uk  Thu Oct 11 09:31:36 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 11 Oct 2012 14:31:36 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
Message-ID: <1349962296.2893.205.camel@balisaur>

Hi Mike
> 
> Internet restored.  Ran the update script and the package list script
> and will forward both to you Tim, the list of things not installed is
> quite long - includes galaxy, raxml and a number of r-cran packages.  

OK, something has definitely jammed then.  Hopefully the log will reveal
the problem (looking at it now).  This also explains why NX didn't work
at all, as the upgrade also does some things to try and fix this.
> 
> We can get around NX for the moment, I'll get people using putty or
> winSCP in the meantime, but it's really helpful for a number of the
> users that are used to desktop environments.  After sorting the
> network connection, NX now working, but it seems much slower than it
> was and various bits of the desktop are missing, sidebar the most
> noticeable.  

The Unity desktop really depends on using the 3D capabilities of your
graphics card and so is really not suitable for NX or remote X in
general, hence you have to use the Gnome fallback as suggested by Tony,
or else move to something like Xfce.  [ I'm not sure how
hard/problematic this could be - not tried it on Ubuntu ].

One thing to bear in mind - and this is useful even if NX desktop is
working perfectly - if that if a user can cope with the command line,
they can set the NX Desktop option to "Custom", click "Settings", set
Options to "Floating Window" and set Application to "gnome-terminal".
Then instead of a full desktop, a terminal window will appear.  If you
run a graphical application from that terminal then that will likewise
appear.  This is faster than a full desktop.
> 
> Users definitely have ssh permissions as
> per http://nebc.nerc.ac.uk/tools/bio-linux/accessing-bio-linux -
> interesting list of stuff after recent NX login in auth.log one of
> which seems to be related to a constant keychain message and the
> screen-saver lock, which doesn't clear with entering the user's
> password.  
> 
Not sure what to make of this.  You mean you have the screensaver
running in the NX desktop window?  I'd just disable it.

More to follow off-list.

Cheers,

TIM

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.

From mikeyj.cox at gmail.com  Thu Oct 11 10:02:44 2012
From: mikeyj.cox at gmail.com (Cox, Michael J)
Date: Thu, 11 Oct 2012 15:02:44 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <1349962296.2893.205.camel@balisaur>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
	<1349962296.2893.205.camel@balisaur>
Message-ID: <1E511FDC-EFD5-4C38-9BC8-7718D0924038@gmail.com>

Cheers Tim,

thanks for the tips.

Just been checking out QIIME - trying OTU picking to check everything's still in place as we're retraining it with Silva - I'm getting an error where it expects a .jar for the classifier to be explicitly called version 2.2 (it's currently looking for it in /usr/share/rdp-classifier.  I think we had this way back during the initial QIIME installation.  

From the package lists I have both rdp-classifier 2.5+repack-3 and bio-linux-rdp-classifier 2:1bl1-1 installed.  I'm guessing the latter is the one that QIIME wants, can you confirm this is version 2.2 and if so I'll edit the name.

Cheers

Mike

On 11 Oct 2012, at 14:31, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Mike
>> 
>> Internet restored.  Ran the update script and the package list script
>> and will forward both to you Tim, the list of things not installed is
>> quite long - includes galaxy, raxml and a number of r-cran packages.  
> 
> OK, something has definitely jammed then.  Hopefully the log will reveal
> the problem (looking at it now).  This also explains why NX didn't work
> at all, as the upgrade also does some things to try and fix this.
>> 
>> We can get around NX for the moment, I'll get people using putty or
>> winSCP in the meantime, but it's really helpful for a number of the
>> users that are used to desktop environments.  After sorting the
>> network connection, NX now working, but it seems much slower than it
>> was and various bits of the desktop are missing, sidebar the most
>> noticeable.  
> 
> The Unity desktop really depends on using the 3D capabilities of your
> graphics card and so is really not suitable for NX or remote X in
> general, hence you have to use the Gnome fallback as suggested by Tony,
> or else move to something like Xfce.  [ I'm not sure how
> hard/problematic this could be - not tried it on Ubuntu ].
> 
> One thing to bear in mind - and this is useful even if NX desktop is
> working perfectly - if that if a user can cope with the command line,
> they can set the NX Desktop option to "Custom", click "Settings", set
> Options to "Floating Window" and set Application to "gnome-terminal".
> Then instead of a full desktop, a terminal window will appear.  If you
> run a graphical application from that terminal then that will likewise
> appear.  This is faster than a full desktop.
>> 
>> Users definitely have ssh permissions as
>> per http://nebc.nerc.ac.uk/tools/bio-linux/accessing-bio-linux -
>> interesting list of stuff after recent NX login in auth.log one of
>> which seems to be related to a constant keychain message and the
>> screen-saver lock, which doesn't clear with entering the user's
>> password.  
>> 
> Not sure what to make of this.  You mean you have the screensaver
> running in the NX desktop window?  I'd just disable it.
> 
> More to follow off-list.
> 
> Cheers,
> 
> TIM
> 
> -- 
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev



From tony.travis at ed.ac.uk  Thu Oct 11 10:25:01 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Thu, 11 Oct 2012 15:25:01 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <1349962296.2893.205.camel@balisaur>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
	<1349962296.2893.205.camel@balisaur>
Message-ID: <5076D6BD.1000103@ed.ac.uk>

On 11/10/12 14:31, Tim Booth wrote:
> [...]
> The Unity desktop really depends on using the 3D capabilities of your
> graphics card and so is really not suitable for NX or remote X in
> general, hence you have to use the Gnome fallback as suggested by Tony,
> or else move to something like Xfce.  [ I'm not sure how
> hard/problematic this could be - not tried it on Ubuntu ].

Hi, Tim.

I've had Unity running under x2go:

   http://www.x2go.org/

This, apparently, is the direction Canonical want Ubuntu to go instead 
of using FreeNX. The snag is that x2go is NOT compatible with NX/FreeNX.

> One thing to bear in mind - and this is useful even if NX desktop is
> working perfectly - if that if a user can cope with the command line,
> they can set the NX Desktop option to "Custom", click "Settings", set
> Options to "Floating Window" and set Application to "gnome-terminal".
> Then instead of a full desktop, a terminal window will appear.  If you
> run a graphical application from that terminal then that will likewise
> appear.  This is faster than a full desktop.

How does that compare with just forwarding X11?

   ssh -CX user at host

To me, the advantage of using a remote NX desktop is that I can work on 
a remote host the same way I would on a local desktop. Launching GUI 
apps from the command-line is how we used to use network transparency. A 
lot of X11 compressing/caching techniques were developed, culminating in 
the NX libraries. These make it practical to use a remote desktop.

>> Users definitely have ssh permissions as
>> per http://nebc.nerc.ac.uk/tools/bio-linux/accessing-bio-linux -
>> interesting list of stuff after recent NX login in auth.log one of
>> which seems to be related to a constant keychain message and the
>> screen-saver lock, which doesn't clear with entering the user's
>> password.
>>
> Not sure what to make of this.  You mean you have the screensaver
> running in the NX desktop window?  I'd just disable it.

I think this might be because a large number of packages 'recommended' 
by ubuntu-desktop are missing. That's what has happended on our server 
install. I'm looking into it, and comparing what Tim's script installed 
with the manifest of the casper filesystem on the Ubuntu 12.04.1 LTS 
Desktop iso.

Bye,

   Tony.


From tbooth at ceh.ac.uk  Thu Oct 11 11:35:11 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 11 Oct 2012 16:35:11 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <5076D6BD.1000103@ed.ac.uk>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
	<1349962296.2893.205.camel@balisaur> <5076D6BD.1000103@ed.ac.uk>
Message-ID: <1349969711.2893.233.camel@balisaur>

Hi,

> I've had Unity running under x2go:
> 
>    http://www.x2go.org/
> 
> This, apparently, is the direction Canonical want Ubuntu to go instead 
> of using FreeNX. The snag is that x2go is NOT compatible with NX/FreeNX.

OK, looks like this is something I need to look into, but since people
like Mike are happy with NX I'll not switch the default system on BL
unless I really have to.

> How does that compare with just forwarding X11?
> 
>    ssh -CX user at host

Doesn't require Windows user to start a separate Exceed (or Xorg)
session.
Significantly faster for some graphical apps, notably Java Swing
interfaces.
Otherwise, not much difference.

> I think this might be because a large number of packages 'recommended' 
> by ubuntu-desktop are missing. That's what has happended on our server 
> install. I'm looking into it, and comparing what Tim's script installed 
> with the manifest of the casper filesystem on the Ubuntu 12.04.1 LTS 
> Desktop iso.

I deliberately only installed the ubuntu-desktop essentials because, as
you said, a lot of the recommended stuff has no place on a server, but
anything needed for remote desktop should indeed go on the list.

Cheers,

TIM


-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.

From tony.travis at ed.ac.uk  Wed Oct 17 17:57:38 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Wed, 17 Oct 2012 22:57:38 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <1349969711.2893.233.camel@balisaur>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
	<1349962296.2893.205.camel@balisaur> <5076D6BD.1000103@ed.ac.uk>
	<1349969711.2893.233.camel@balisaur>
Message-ID: <507F29D2.1000601@ed.ac.uk>

On 11/10/12 16:35, Tim Booth wrote:
> Hi,
>
>> I've had Unity running under x2go:
>>
>>     http://www.x2go.org/
>>
>> This, apparently, is the direction Canonical want Ubuntu to go instead
>> of using FreeNX. The snag is that x2go is NOT compatible with NX/FreeNX.
>
> OK, looks like this is something I need to look into, but since people
> like Mike are happy with NX I'll not switch the default system on BL
> unless I really have to.
>
>> How does that compare with just forwarding X11?
>>
>>     ssh -CX user at host
>
> Doesn't require Windows user to start a separate Exceed (or Xorg)
> session.
> Significantly faster for some graphical apps, notably Java Swing
> interfaces.
> Otherwise, not much difference.
>
>> I think this might be because a large number of packages 'recommended'
>> by ubuntu-desktop are missing. That's what has happended on our server
>> install. I'm looking into it, and comparing what Tim's script installed
>> with the manifest of the casper filesystem on the Ubuntu 12.04.1 LTS
>> Desktop iso.
>
> I deliberately only installed the ubuntu-desktop essentials because, as
> you said, a lot of the recommended stuff has no place on a server, but
> anything needed for remote desktop should indeed go on the list.

Hi, Tim.

Sorry for the delay in getting back to you about NX, but it took me a 
while to work out what was wrong. I notice that you install 
"freenx-server", instead of "freenx", and that the indicator panel is 
missing. The terminal font is unreadable (overlapping letters) and there 
is no "logout" button. I worked around the font problem by editing the 
default terminal proble and installed "indicator-applet-complete" to 
provide a logout button in the top right corner. I've now got NX in a 
more-or-les workable configuration, but I'm concerned that this did not 
happen when I installed "ubuntu-desktop" and "FreeNX" on an Ubuntu 12.04 
LTS server instance manually (i.e. without your upgrade script).

BTW, I used my "dpkg-dsel" script to compare what your script installs 
in comparison to the 64-bit Ubuntu-desktop 12.04.1 LTS casper manifest.

HTH,

   Tony.


From tony.travis at ed.ac.uk  Wed Oct 17 19:42:17 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Thu, 18 Oct 2012 00:42:17 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <507F29D2.1000601@ed.ac.uk>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<CACwm78MNHHFuusVZ+fOdReZ1gxXdg70m1_5bg0K30wrHqzstfQ@mail.gmail.com>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
	<1349962296.2893.205.camel@balisaur> <5076D6BD.1000103@ed.ac.uk>
	<1349969711.2893.233.camel@balisaur> <507F29D2.1000601@ed.ac.uk>
Message-ID: <507F4259.8020707@ed.ac.uk>

On 17/10/12 22:57, Tony Travis wrote:
> [...]
> Sorry for the delay in getting back to you about NX, but it took me a
> while to work out what was wrong. I notice that you install
> "freenx-server", instead of "freenx", and that the indicator panel is
> missing. The terminal font is unreadable (overlapping letters) and there
> is no "logout" button. I worked around the font problem by editing the
> default terminal proble and installed "indicator-applet-complete" to
> provide a logout button in the top right corner. I've now got NX in a
> more-or-les workable configuration, but I'm concerned that this did not
> happen when I installed "ubuntu-desktop" and "FreeNX" on an Ubuntu 12.04
> LTS server instance manually (i.e. without your upgrade script).

Hi, Tim.

I've resolved the font problems when running the Gnome fall-back session 
under NX, but you're not going to like my solution!

Ubuntu/Debian now install 'recommends' by default. However, your script 
does not and only installs the bare minimum. In particular, it does not 
install terminal fonts or, as noted previously, the indicator applet.

I want to deploy a full Bio-Linux 7 desktop on a terminal server, so 
I've forced the installation of all "ubuntu-desktop" recommends:

> aptitude purge ubuntu-desktop
> aptitude install ubuntu-desktop
> aptitude purge network-manager network-manager-gnome network-manager-pptp network-manager-pptp-gnome

Note: The "network-manager*" packages should not be installed on a 
server. However, the other "ubuntu-desktop" recommends are as useful on 
a Bio-Linux terminal server as they are on a stand-alone Bio-Linux 
laptop/desktop.

Next task - How to backup properly: WHY use "nepomuk" from KDE?

Even the default, duplicity-based, Ubuntu backup is better than that!

Bye,

   Tony.



From tony.travis at ed.ac.uk  Wed Oct 17 20:05:48 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Thu, 18 Oct 2012 01:05:48 +0100
Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <507F4259.8020707@ed.ac.uk>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
	<1349962296.2893.205.camel@balisaur> <5076D6BD.1000103@ed.ac.uk>
	<1349969711.2893.233.camel@balisaur>
	<507F29D2.1000601@ed.ac.uk> <507F4259.8020707@ed.ac.uk>
Message-ID: <507F47DC.8080609@ed.ac.uk>

On 18/10/12 00:42, Tony Travis wrote:
> [...]
> Next task - How to backup properly: WHY use "nepomuk" from KDE?
>
> Even the default, duplicity-based, Ubuntu backup is better than that!

Hi, Tim.

[Grovel] Sorry, I didn't notice that you included my backup script ;-)

However, I bet I'm not the only one who gets caught out seeing "nepomuk 
backup" on the BL7 system admin menu...

Bye,

   Tony.


From tbooth at ceh.ac.uk  Thu Oct 18 04:58:01 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 18 Oct 2012 09:58:01 +0100
Subject: [Bio-linux-dev] NX and Backups
In-Reply-To: <507F47DC.8080609@ed.ac.uk>
References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk>
	<506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk>
	<506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk>
	<50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk>
	<1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk>
	<CACwm78NXOFpTHSYV=cA_9pVBpBkZvP62CUgyPtGy-f=HXf84xw@mail.gmail.com>
	<1348743818.4031.24.camel@balisaur>
	<CACwm78NZXzDGB=aE2tqs+9+5rHhYOdPTkR-ruVjMWUgBujY5tw@mail.gmail.com>
	<1348764601.4031.80.camel@balisaur>
	<CALenahkfAR8h8mjf00tp7=Bf1W22cR4WP_0Vv9NSK87UyY23bw@mail.gmail.com>
	<1349097289.24717.1.camel@balisaur>
	<CAKaWfX3fG5Kmog4XPqhytF_Mo7o==NaM=Lsk5TzCh3c28GKGnw@mail.gmail.com>
	<50769A00.5020500@ed.ac.uk>
	<92E0B035-4A94-4B01-A19D-ACC0AAEA264A@gmail.com>
	<1349962296.2893.205.camel@balisaur> <5076D6BD.1000103@ed.ac.uk>
	<1349969711.2893.233.camel@balisaur>	<507F29D2.1000601@ed.ac.uk>
	<507F4259.8020707@ed.ac.uk> <507F47DC.8080609@ed.ac.uk>
Message-ID: <1350550681.3081.128.camel@balisaur>

Hi Tony,

I did indeed keep the bio-linux-backups, with your TOH backup pattern,
but I would also assume that users looking for backup in the Gnome
control panel would find Deja Dup (Duplicity) which is the standard
Ubuntu backup tool.  I'm not sure where "nepomuk" is appearing from but
I shall find it and smite it!

Thanks for the continued help on NX.  I'll ensure I have everything
properly tested for remote access before I take BL7 out of beta testing.

Cheers,

TIM

On Thu, 2012-10-18 at 01:05 +0100, Tony Travis wrote:
> On 18/10/12 00:42, Tony Travis wrote:
> > [...]
> > Next task - How to backup properly: WHY use "nepomuk" from KDE?
> >
> > Even the default, duplicity-based, Ubuntu backup is better than that!
> 
> Hi, Tim.
> 
> [Grovel] Sorry, I didn't notice that you included my backup script ;-)
> 
> However, I bet I'm not the only one who gets caught out seeing "nepomuk 
> backup" on the BL7 system admin menu...
> 
> Bye,
> 
>    Tony.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-- 
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
-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.

From tbooth at ceh.ac.uk  Wed Oct 31 11:54:44 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 31 Oct 2012 15:54:44 +0000
Subject: [Bio-linux-dev] Fwd:  Upgrade to Bio-Linux 7 (at last)
In-Reply-To: <0D9F3C8D-6147-41AE-8482-9E59DC3470AF@gmail.com>
References: <1E511FDC-EFD5-4C38-9BC8-7718D0924038@gmail.com>
	<0D9F3C8D-6147-41AE-8482-9E59DC3470AF@gmail.com>
Message-ID: <1351698884.3081.496.camel@balisaur>

Hi Mike,

You shouldn't need to rename any files to make Qiime work, and if you do
rename any file owned by a package it will interfere with updates so
this is best avoided.  The path to the RDP classifier is set in the file
/usr/lib/qiime/shell/qiime_environment and it should be set
to /usr/share/rdp-classifier/rdp_classifier.jar unless you override it
with your own environment variable.  Nothing in the current Qiime
package refers to the version 2.2 jar explicitly.

I'm wondering if you had a similar problem before and you set
$RDP_CLASSIFIER manually but the setting you have is now wrong as I've
neatened things up a bit.  Can you please try doing "echo
$RDP_CLASSIFIER" both in a regular shell and at a QIIME shell prompt?
Then in a regular prompt try "env -u RDP_CLASSIFIER qiime" and again
"echo $RDP_CLASSIFIER" at the prompt.  That should reveal what is going
on.

Cheers,

TIM

On Wed, 2012-10-31 at 11:01 +0000, Michael Cox wrote:
> Hi Tim,
> 
> 
> I forgot to follow the below issue up with you whilst your were
> tackling the update - does the classifier need updating, or am I OK
> just to change the name of it?
> 
> 
> Thanks
> 
> 
> Mike
> 
> Begin forwarded message:
> 
> > From: "Cox, Michael J" <mikeyj.cox at gmail.com>
> > 
> > Subject: Re: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
> > 
> > Date: 11 October 2012 15:02:44 BST
> > 
> > To: Bio-Linux technical discussion
> > <bio-linux-dev at nebclists.nerc.ac.uk>
> > 
> > 
> > Cheers Tim,
> > 
> > thanks for the tips.
> > 
> > Just been checking out QIIME - trying OTU picking to check
> > everything's still in place as we're retraining it with Silva - I'm
> > getting an error where it expects a .jar for the classifier to be
> > explicitly called version 2.2 (it's currently looking for it
> > in /usr/share/rdp-classifier.  I think we had this way back during
> > the initial QIIME installation.  
> > 
> > From the package lists I have both rdp-classifier 2.5+repack-3 and
> > bio-linux-rdp-classifier 2:1bl1-1 installed.  I'm guessing the
> > latter is the one that QIIME wants, can you confirm this is version
> > 2.2 and if so I'll edit the name.
> > 
> > Cheers
> > 
> > Mike
> > 


-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.