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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