[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
Mike Cox
mikeyj.cox at gmail.com
Thu Oct 11 04:29:22 EDT 2012
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
>
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