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:
- 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.
- 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.goecks@emory.edu> wrote:
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