[Bio-linux-dev] tophat2

[William Spooner]

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
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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
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>>> 
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>> ---
>> 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
> _______________________________________________
> 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/