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
*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

--
Jennifer Hillman-Jackson
http://galaxyproject.org

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