bedtools and galaxy

[Davide Cittaro]

Hi there, I may have missed some post, did anybody manage to write bedtools definitions for galaxy?

d

/*

Davide Cittaro

Cogentech - Consortium for Genomic Technologies

via adamello, 16

20139 Milano

Italy

tel.: +39(02)574303007

e-mail: davide....@ifom-ieo-campus.it

*/

[Aaron Quinlan]

Hi Davide,
Gordon Assaf has added genomeCoverageBed to his local installation of
Galaxy at CSHL. see: http://groups.google.com/group/bedtools-discuss/browse_thread/thread/e3be681586693399

I had planned to create Galaxy wrappers for all of BEDTools based on
his nice example, but have yet to do so. I haven't pushed too hard on
this as the Galaxy folks have many similar tools. That said, the
functionality of intersecting BAM and BED or GFF (and soon VCF) does
not exist in Galaxy.

Is this an urgent need for your local installation?

Aaron

On Jul 1, 1:47 pm, Davide Cittaro <davide.citt...@ifom-ieo-campus.it>
wrote:

> Hi there, I may have missed some post, did anybody manage to write bedtools definitions for galaxy?
>
> d
> /*
> Davide Cittaro
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007

> e-mail: davide.citt...@ifom-ieo-campus.it
> */

[Assaf Gordon]

Hi Davide,

I'm slowly starting to write more wrappers for some of the tools (I don't currently need them all),
I'll post them as they become available.
If you (or others) are interested in working together on this, let me know.

Next I'll probably add "windowBed" .
-gordon

[Aaron Quinlan]

Perhaps posting the wrappers as a separate package on the BEDTools site would be beneficial? I'd be glad to help in two weeks time.

I see intersectBed, coverageBed, windowBed, and genomeCoverageBed being the biggest bang for the buck initially.

[Davide Cittaro]

On Jul 1, 2010, at 11:07 PM, Aaron Quinlan wrote:

Is this an urgent need for your local installation?

No, it's not :-) Yesterday I've written a short wrapper of 4 piped bedtools to go from bam to bigWig and I've wondered if bedtools might be included into galaxy. As they are in C++ they perform much better than pythonic tools and, AFAIK, all the functionalities are included...

Thanks

d

/*

Davide Cittaro

Cogentech - Consortium for Genomic Technologies

via adamello, 16

20139 Milano

Italy

tel.: +39(02)574303007

e-mail: davide....@ifom-ieo-campus.it

*/