[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas
raonyguimaraes at gmail.com
Sat Sep 29 09:14:29 EDT 2012
Hello Tim and everyone else!
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 <http://ubuntustudio.org/tour/audio/>,Graphics
<http://ubuntustudio.org/tour/graphics/>,Video
<http://ubuntustudio.org/tour/video/>,
Photography<http://ubuntustudio.org/tour/photography/>and Publishing
<http://ubuntustudio.org/tour/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
The bl_do_update_to7.sh<http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh>worked
really well and I'm glad to have all the ecosystem from Ubuntu
Studio 12.04 back on my laptop this time mixed all the packages from
Biolinux 7.
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 ?)
For me, the biggest difference of Biolinux 6 was the menu full of apps for
bioinformatics already installed that may be I would never really discover
by myself and that I could simply give a try without fearing breaking my
system when installing it. Let alone the fact I could show off to my
friends all the cool stuff I had installed for doing my research and
analysis. :D Thank you a lot for this guys!
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.
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
Thank you all and keep the good work!
Regards.
Atenciosamente,
C------0 Raony Guimarães Corrêa Do Carmo Lisboa Cardenas
G--------1
T--------1 msn/gtalk: raonyguimaraes at gmail.com
A-------0 skype: raonyguimaraes
C----0 phone: +55 31 93404152
1
0--G Member @ LGC - Laboratory of Clinical Genomics
1-----T Bachelor in Biomedical Informatics - USP Ribeirão Preto
1--------A PhD Student in Bioinformatics - UFMG
0---------C
1--------G Creator of the Brazilian Portal of Biomedical Informatics and
Medicina do Futuro
1-----G www.informaticabiomedica.org / www.medicinadofuturo.com.br
T
G--0 Research Interests: Personalized Medicine and
Pharmacogenomics
A------0 http://lattes.cnpq.br/0263349039132540
T--------1
C--------0 "Bioinformatics: We Can Change The World..."
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
>
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