Ok,

So I guess I need to install it locally or in the cloud to use certain tools, 
right?

Thanks!

From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Monday, December 16, 2013 6:55 PM
To: Javier Simon-Sanchez; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Count intervals in one file overlapping intervals in 
another file

Javier,

This is part of a tool repository that can be installed into a local, cloud, or 
slipstream Galaxy and used there.

http://getgalaxy.org
http://usegalaxy.org/cloud
https://wiki.galaxyproject.org/BigPicture/Choices
http://usegalaxy.org/toolshed
https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance

I am not sure of the size of your files, but if not too large, these tools may 
work just fine on a local install on a laptop. For anything larger, a server 
would be needed for a local or for the easiest set-up, use a cloud. For ongoing 
work, a slipstream Galaxy can be a great solution for labs.

Take care,

Jen
Galaxy team
On 12/16/13 7:30 AM, Javier Simon-Sanchez wrote:
Hi Jennifer,

Intersect_bed is exactly what I need. How can I include this on my workflows? 
(sorry for asking so many things. Im new with galaxy)

From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Monday, December 16, 2013 4:03 PM
To: Javier Simon-Sanchez; galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>
Subject: Re: [galaxy-dev] Count intervals in one file overlapping intervals in 
another file

Hello Javier,

If you would like to see an enhancement for a tool that is sourced from the 
tool shed, then the repository author is the correct person to contact. Go to 
http://usegalaxy.org/toolshed and log in to see contact information. The repo 
name is "bedtools".

The Tool Shed also has an alternate versions of some BedTools, including this 
one. An alternative has an option to set overlap length: " bed_intersect".

Also, there are tools in the group "Operate on Genomic Intervals". I don't know 
the details of your query, but these tools may also be helpful.

Best,

Jen
Galaxy team
On 12/13/13 2:41 AM, Javier Simon-Sanchez wrote:
Hello,

I just noticed that when using the above mentioned option, it is not possible 
to set a minimum overlap required. This option can be run in the command line 
version of BEDtools and I think is crucial. Could you please implement it in 
Galaxy?

Thanks a lot.

-------------------------------------
Javier Simón-Sánchez, PhD
Research Scientist
MRC-Holland
Willem Schoutenstraat 6
1057 DN, Amsterdam
The Netherlands






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Jennifer Hillman-Jackson

http://galaxyproject.org
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