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
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
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?
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