[Bio-linux-dev] tophat2

[William Spooner]

Thanks Tim,

Actually, there is; bowtie2 is a big update and there are still people who want to use the 'original' bowtie in established workflows. I've found bowtie2 has a different memory profile which can cause problems, but I expect it's worth it for the extra sensitivity.

Will

On 6 Dec 2012, at 18:34, Tim Booth wrote:

> 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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>>> 
>>> -- 
>>> 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/
>> 
>> _______________________________________________
>> Bio-Linux-dev mailing list
>> Bio-Linux-dev at nebclists.nerc.ac.uk
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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/