[Bio-linux-dev] tophat2

[Tim Booth]

Hi Will,

Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't see
that the new version was available.  I wonder if there's any reason you
might want both at once?

I'll have a try rebuilding it now.

Cheers,

TIM

On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:
> Hi Tim,
> 
> Many thanks for taking care of this.
> 
> I've finally got around to trying it out. tophat seems to be the at version 2 (as is cufflinks);
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/
> 
> bowtie, however, is languishing on version 0;
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/
> 
> Is this as expected?
> 
> Thanks,
> 
> Will
> 
> 
> On 14 Nov 2012, at 14:48, Tim Booth wrote:
> 
> > Hi,
> > 
> > I've pushed the updates to all these and Velvet, so everything should be
> > current now.
> > 
> > Cheers,
> > 
> > TIM
> > 
> > On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
> >> Many thanks Tim,
> >> 
> >> We'll test that tomorrow. I presume it's the complete bowtie2/tophat2/cufflinks2 stack?
> >> 
> >> Will
> >> 
> >> On 13 Nov 2012, at 16:58, Tim Booth wrote:
> >> 
> >>> Hi Will,
> >>> 
> >>> The TopHat package maintained by Debian Med is up-to-date and seems to
> >>> build fine on Ubuntu, so I've pushed a newer version to the Bio-Linux
> >>> PPA.  Anyone who already upgraded to BL7 will get the update
> >>> automatically.
> >>> 
> >>> Cheers,
> >>> 
> >>> TIM
> >>> 
> >>> On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
> >>>> One for Tim, Brad,
> >>>> 
> >>>> What is the status of tophat2 packaging for BL? Google suggests that Brad is working on something. Anything we can do to help?
> >>>> 
> >>>> Thanks,
> >>>> 
> >>>> Will
> >>>> 
> >>>> ---
> >>>> William Spooner                          http://eaglegenomics.com
> >>>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> >>>> 
> >>>> _______________________________________________
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> >>> 
> >>> -- 
> >>> 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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> >> 
> >> ---
> >> William Spooner                          http://eaglegenomics.com
> >> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> >> 
> >> _______________________________________________
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> >> 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
> 
> ---
> William Spooner                          http://eaglegenomics.com
> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> 
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-- 
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