Here's my first run at adding genomeCoverageBed to Galaxy.
The necessary files are here:
http://cancan.cshl.edu/labmembers/gordon/files/galaxy_BEDTools_2010_05_26.tar.bz2
You can experiment with it by going here:
http://cancan.cshl.edu/publicgalaxy/
And selecting "BedTools" (at the bottom left side).
This is just a testing server, so it's slow. It is meant to show our tools, not to analyze real data.
The "exons" and "strands" options require the patch I've sent you.
The tool automatically uses the correct "chrom.sizes" file based on the organism of the dataset (called "dbkey" or "database" in galaxy).
I've prepared a 'chrom_size' for every standard organism I could find in UCSC (they are in the tarball, inside "tool-data").
This way, the user doesn't need to worry about this issue, as long as the organism is set.
Comments and welcomed,
-gordon
Perhaps I should try to create XML entries for each BEDTool so that others can add them to their local Galaxy instances as well. I may also pass on the setup to the Galaxy folks, especially for the tools that don't exist on it or those that offer add'l functionality.
I appreciate you passing this on.
By the way, I plan to integrate your changes in the next release; just trying to find time to finish it up (likely late June).
Best,
Aaron