I have been browsing the Galaxy wiki pages and they mention galaxy wrappers for several assembly tools, like Velvet, Trinity and Abyss, but I couldn't find the documentation on how to have them working on the cloud.
There is a Galaxy cloud screencast, but I couldn't find detailed instructions on where to find the assembly wrappers code (this url gives me a 404: http://community.g2.bx.psu.edu/) and how to set them up for a Galaxy Cloud instance. Anyone?
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As far as I know assembly is not offered in the default Galaxy server due to the unpredictable amount of computing resources that an assembly may require. So you would need to run a custom Galaxy instance while deploying your own tools.
There are several publicly accessible servers that support assembly. See http://bit.ly/gxypublic My memory is that CBIIT and Andromeda do.
The Galaxy cloud instance supports Velvet when it first comes up. See http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted for almost up-to-date instructions on how to set up a coud instance at AWS.
If you have your own Galaxy instance there are several tools in the tool shed you can use. See http://bit.ly/gxyshed and click on Assembly.
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