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


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Bioinformatics Core Facility University of Manchester
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<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


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