Question: Homer for Motif search
1
gravatar for sjn
18 months ago by
sjn10
sjn10 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 • 357 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson22k • written 18 months ago by sjn10
0
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson22k 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 COMMENTlink modified 18 months ago • written 18 months ago by Jennifer Hillman Jackson22k
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