Attached to the card, thanks Peter.

J.

On Feb 28, 2013, at 11:14 AM, Peter Briggs wrote:

> Hi Jeremy
> No problem - zip file with the two patches is attached, please let me know if 
> there's a problem.
> Best wishes
> Peter
> 
> On 28/02/13 15:07, Jeremy Goecks wrote:
>> Hmm, I don't see a patch for your changes to the wrapper script. Can you 
>> please bundle up and send along your tool definition + wrapper script 
>> changes and I'll add it to the card?
>> 
>> Thanks,
>> J.
>> 
>> On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote:
>> 
>>> Hi Jeremy - that's awesome, thanks!
>>> 
>>> One thing: not sure if I read this right (I'm a Trello newbie) however it 
>>> looks like only the patch to the tool XML has was attached to the card. 
>>> This change also requires a patch to the python wrapper script (should have 
>>> been attached to my earlier message).
>>> 
>>> Apologies if I missed something, thanks again
>>> 
>>> Best wishes, Peter
>>> 
>>> On 27/02/13 18:33, Jeremy Goecks wrote:
>>>> Thanks Peter. I've added your patch to the Trello card tracking 
>>>> incorporation of community contributions to the Bowtie wrapper:
>>>> 
>>>> https://trello.com/c/TdYxdbkm
>>>> 
>>>> Best,
>>>> J.
>>>> 
>>>> On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
>>>> 
>>>>> Hello Alexander
>>>>> 
>>>>> I've made some changes to our local copy of the bowtie tool files 
>>>>> (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of 
>>>>> capturing bowtie's stderr output and adding it as an additional history 
>>>>> item (here the statistics in this output is used as input to a local 
>>>>> tool).
>>>>> 
>>>>> I've attached patches to the tool in case they're any use to you.
>>>>> 
>>>>> (As an aside and more generally: I'm not sure how to manage these local 
>>>>> customisations in the longer term - what do other people on this list do?)
>>>>> 
>>>>> HTH, best wishes, Peter
>>>>> 
>>>>> On 25/02/13 11:29, Alexander Kurze wrote:
>>>>>> Hello,
>>>>>> 
>>>>>> I am using the bowtie-wrapper on my locally installed galaxy server to
>>>>>> align reads. However I missing the stats read-out. Is there any
>>>>>> possibility to include statistics about unaligned reads?
>>>>>> 
>>>>>> If I use bowtie vi comman line I get following output:
>>>>>> 
>>>>>> 
>>>>>>> bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam
>>>>>> End-to-end 2/3-mismatch full-index search: 01:00:21
>>>>>> # reads processed: 12084153
>>>>>> # reads with at least one reported alignment: 9391748 (77.72%)
>>>>>> # reads that failed to align: 2692405 (22.28%)
>>>>>> Reported 30293838 alignments to 1 output stream(s)
>>>>>> 
>>>>>> 
>>>>>> The output should be normally saved in the stderr but unfortunatly the
>>>>>> stderr is somehow deleted after the alignment job is done in bowtie
>>>>>> under galaxy.
>>>>>> 
>>>>>> Any idea how I can still access the stats?
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Alex
>>>>>> 
>>>>>> --
>>>>>> Alexander Kurze, DPhil
>>>>>> University of Oxford
>>>>>> Department of Biochemistry
>>>>>> South Parks Road
>>>>>> Oxford, OX1 3QU
>>>>>> United Kingdom
>>>>>> 
>>>>>> Tel: +44 1865 613 230
>>>>>> Fax:+44 1865 613 341
>>>>>> 
>>>>>> 
>>>>>> ___________________________________________________________
>>>>>> Please keep all replies on the list by using "reply all"
>>>>>> in your mail client.  To manage your subscriptions to this
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>>>>>> 
>>>>>>   http://lists.bx.psu.edu/
>>>>>> 
>>>>> 
>>>>> --
>>>>> Peter Briggs peter.bri...@manchester.ac.uk
>>>>> Bioinformatics Core Facility University of Manchester
>>>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>>>> 
>>>>> 
>>>>> <bowtie_wrapper.xml.patch>
>>>> 
>>> 
>>> --
>>> Peter Briggs peter.bri...@manchester.ac.uk
>>> Bioinformatics Core Facility University of Manchester
>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>> 
>>> 
>> 
> 
> -- 
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> 
> 
> <bowtie_wrapper_patches_pjbriggs.zip>


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