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Question: Homer for Motif search
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gravatar for sjn
2.9 years ago by
sjn • 10
sjn • 10 wrote:

Hi,

   I would like to use HOMER to search for enriched motif on a ChIPseq analysis I did using Galaxy. How can I use the tool that is available in Toolshed. From basic search I found that one can add anything from Toolshed to local galaxy by signing in as admin. But I am using public server and my account do not have admin option. Any suggestions?

 
galaxy • 783 views
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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by sjn • 10
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Public servers have a fixed set of tools set by the owners/administrators. Tools choices are often based on the available compute these groups have available to share with public users and/or the servers focus on specific analysis pathways. Galaxy Main (http://usegalaxy.org) will not be including HOMER for at least the near term. You can reach out to other groups and ask about their plans directly: PublicGalaxyServers

Setting up a Local Galaxy and adding tools is designed to a be a simple process. The key requirement for successful tool execution is providing enough compute resource. In the most general terms, the resource required by a tool when executed line-command is roughly the same as Galaxy would require to execute it. See any tool's manual for computing requirements (or the tool author's support channels/forums).

The other option is to use a Cloud Galaxy. AWS offers research grants to help with costs.

Both options are covered here: https://wiki.galaxyproject.org/BigPicture/Choices and here https://wiki.galaxyproject.org/Support#About_Galaxy

Hope one of these works out for you! Jen, Galaxy team
ADD COMMENT • link modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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