[Bio-linux-dev] EMBOSS and Perl libraries

[Tim Booth]

Hi Joachim,

Thanks for the feedback.

I'm not sure why you would have had that problem with EMBOSS, but we've
substantially changed the way EMBOSS is packaged since BL5 so the
problem may well have simply gone away.  We can no longer provide the
EMBOSS KMenus (the GUI that used to appear when you selected a single
app from the Applications menu) so you'd now have to use JEmboss as the
GUI in any case.  I'll make sure this is tested on the live image.

The two Perl packages are very small so I've added them to the default
image for the final release at your suggestion.

Cheers,

TIM

On Fri, 2010-05-21 at 08:43 +0100, Joachim Jacob wrote:
> Hello,
> 
> I have used Biolinux 5 for a three day training session I organized at
> VIB (www.bits.vib.be).
> It helped us a lot - thanks. During the training we started with
> installing Biolinux5 as a virtual machine (virtualbox).
> Updates were not performed. This vm was used during the whole course.
> 
> One question though: although the emboss GUI was present, we had to
> install emboss again to make it work.
> $ sudo apt-get install emboss
> 
> The original installation was apparently not found.
> 
> Also: we required for perl two additional packages:
> perl-class-inspector and
> libfile-slurp-perl
> 
> Thanks and regards,
> Joachim.
> 
> 
> On 20/05/10 13:00, bio-linux-dev-request at nebclists.nerc.ac.uk wrote: 
> > Send Bio-Linux-dev mailing list submissions to
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> > Today's Topics:
> > 
> >    1. Re: bio-linux-backups (Tony Travis)
> > 
> > 
> > ----------------------------------------------------------------------
> > 
> > Message: 1
> > Date: Wed, 19 May 2010 15:22:41 +0100
> > From: Tony Travis <a.travis at abdn.ac.uk>
> > Subject: Re: [Bio-linux-dev] bio-linux-backups
> > To: bio-linux-dev at nebclists.nerc.ac.uk
> > Message-ID: <4BF3F431.7050101 at abdn.ac.uk>
> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> > 
> > On 17/05/10 09:32, Tim Booth wrote:
> >   
> > > Hi Tony,
> > > 
> > > Yes, I changed the setup script to run 'mkfs.ext4' instead of
> > > 'mkfs.ext3' as you suggested.
> > > [...]
> > >     
> > Hello, Tim.
> > 
> > Although /backups itself is now on an ext4 filesystem, your "backup" 
> > script" does not detect or dump Bio-Linux on ext4 filesystems ;-)
> > 
> > Attached is a patch to show the differences between your backup script 
> > and mine: I have a configuration file in /etc/default, and use ETOH.
> > 
> > Bye,
> > 
> >    Tony.
> >   
> 
> -- 
> 
> BITS logo     
> 
> Joachim Jacob, PhD.
> Bioinformatics Trainer
> BITS - www.bits.vib.be     
> VIB - www.vib.be
> VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium  (see
> map)
> Tel.: +32 9 244 66 11     Fax.: +32 9 244 66 10 
> 
> 
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+44 1491 69 2705


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