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Re-re-visit how Galaxy modules are imported. #56

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Jan 13, 2015
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Should prevent Galaxy from failing to load if planemo's virtual environment is not deactivated. Eliminates some of the terrible hacks related to de-activating planemo's virutalenv before starting Galaxy (though admittedly introduces its own terrible hack of planemo's runtime sys.path in the CLI load point).

Should close #50 and #55 and is a better response to #47.

Hack planemo's sys.path instead of essentially hacking externally so that Planemo's variant of galaxy modules can never affect external Galaxy calls.
... no longer needed because Planemo's PYTHONPATH doesn't need to conflict with Galaxy's - planemo adds the proper modules at runtime not prior to execution.
1) Make implicit dependency on virtualenv optional.
2) Don't run common_startup.sh - this is done inside of run_tests.sh now.
jmchilton added a commit that referenced this pull request Jan 13, 2015
Re-re-visit how Galaxy modules are imported.
@jmchilton jmchilton merged commit 4250874 into master Jan 13, 2015
jmchilton added a commit that referenced this pull request Jan 13, 2015
... I believe this is no longer a problem after pull request #56.
@jmchilton jmchilton deleted the restructure_galaxy branch March 3, 2015 21:41
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Error with test if --galaxy_root is a fresh Galaxy clone
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