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

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merged 3 commits into from Jan 13, 2015

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jmchilton commented Jan 13, 2015

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.

jmchilton added some commits Jan 13, 2015

Restructure how galaxy submodules are imported.
Hack planemo's sys.path instead of essentially hacking externally so that Planemo's variant of galaxy modules can never affect external Galaxy calls.
Eliminate hacking of planemo virtualenv at runtime...
... 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.
Improvements to --install_galaxy.
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

Merge pull request #56 from galaxyproject/restructure_galaxy
Re-re-visit how Galaxy modules are imported.

@jmchilton jmchilton merged commit 4250874 into master Jan 13, 2015

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jmchilton added a commit that referenced this pull request Jan 13, 2015

Eliminate scary warning about planemo's virtualenv...
... I believe this is no longer a problem after pull request #56.

@jmchilton jmchilton deleted the restructure_galaxy branch Mar 3, 2015

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