First off thank you heartily for pointing me in the right direction here. It SEEMS like i have managed to accomplish this. Meaning: i finally got the run to get past the parsing of the config file and now have a process running on the cpu and the server log shows a command line string that matches what I was trying to get. However I am VERY new at the whole Cheetah craziness, so I DEF want you folks to double check my work.
I would LOVE to contribute a patch but have these questions and concerns: 1. I cloned the 'dist' branch not the 'central' branch originally and am not sure if my tophat_wrapper.xml version will clash with any that have been included in the central branch, I would assume that the system's diff capabilities SHOULD be able to sort this out but I am WAY more familiar with git than hg. 2. I have created a bitbucket account and supplied my pubkey, but I dont see anything on the wiki that describes how a person gets "push" or similar permissions on the galaxy project what is the procedure for correctly submitting these types of piecemeal single file changes? Thanks again for your help and I am very excited to have a chance to give back! Gus On Mon, Jul 11, 2011 at 8:51 AM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote: > > I recommend to use the repeat tag (see > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the > existing parameter to make it possible to select multiple files. > > Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example > of how to use this tag. > > Gus, if you end up modifying the Tophat wrapper to support multiple input > datasets, please submit a patch or fork galaxy-central via bitbucket and > I'll integrate these enhancements into the Galaxy code base as this would be > nice functionality to have. > > Best, > J. -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*
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