We have set up our local Galaxy installation to submit jobs by default through 
HTCondor, using the drmaa tool runner.  We override this on a tool-by-tool 
basis in universe_wsgi.ini, to specify certain tools we always want to run 
locally.

The problem is that EMBOSS tools have a tool id like 'emboss: infoseq46', and 
it's not possible to reference a tool with an id containing a colon in the 
universe_wsgi.ini file (because colon is the character which separates a 
configuration item name from its value).

It seems to me there are two possible solutions:
1. Implement some form of escape character processing in the config file parser 
(on top of Python's ConfigParser) so we can write tool ids in that file like 
'emboss%3a infoseq46'
2. Change all the EMBOSS tools to have ids like 'emboss-infoseq46' rather than 
using a colon and space.

For now, we are modifying our XML files locally (with a script) to do 2.

Are there any comments from Galaxy developers on which of these solutions they 
prefer, or any reason why (2) shouldn't be incorporated in the Galaxy mainline?

cheers,
Simon


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