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Question: VISPA available on Galaxy
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gravatar for alberto.gil.12
4.0 years ago by
alberto.gil.12 • 10
United Kingdom
alberto.gil.12 • 10 wrote:

Hello, 

I was wondering whether there is any plan to implement VISPA (pipeline for the identification of vector integration sites) within the Galaxy tools in the near future.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169225/

Thank you, 

Albert
galaxy • 686 views
ADD COMMENT • link •
modified 4.0 years ago • written 4.0 years ago by alberto.gil.12 • 10
1

Not that I'm aware of it ... but I can help you to implement it :)

ADD REPLY • link written 4.0 years ago by Bjoern Gruening ♦ 5.1k

That would be great, do I need a hadoop cluster though?

Thanks, 

ADD REPLY • link written 4.0 years ago by alberto.gil.12 • 10

Thank you Simone. 

ADD REPLY • link written 4.0 years ago by alberto.gil.12 • 10
1
gravatar for simone.leo
4.0 years ago by
simone.leo • 10
Italy
simone.leo • 10 wrote:

Source code for VISPA, includng Galaxy tools, is available at https://github.com/crs4/vispa
ADD COMMENT • link written 4.0 years ago by simone.leo • 10

Is there some blockage we can help with so it can be put in the ToolShed? 

ADD REPLY • link written 4.0 years ago by Martin Čech ♦♦ 4.9k

Galaxy wrappers do not define tests. Moreover, resolving dependencies is not extremely easy. And yes, you do need a Hadoop cluster if you want the alignment and filtering section to scale.

ADD REPLY • link written 4.0 years ago by simone.leo • 10
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