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Activate mulled dependencies once per job #4945

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merged 2 commits into from Nov 6, 2017

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nsoranzo commented Nov 6, 2017

Fix #4821 by using an OrderedSet of dependencies instead of list.

Also, remove requirement from shell_commands() parameters to make Dependency classes self-contained.

Superseeds #4932.

nsoranzo and others added some commits Nov 6, 2017

Return an OrderedSet of dependencies instead of a list
This avoids activating mulled dependencies multiple times and fixes
#4821. We use OrderedSet because
the order of activation may matter for toolshed dependencies.

@galaxybot galaxybot added the triage label Nov 6, 2017

@galaxybot galaxybot added this to the 18.01 milestone Nov 6, 2017

@mvdbeek

mvdbeek approved these changes Nov 6, 2017

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jmchilton commented Nov 6, 2017

Reviewed pulsar, planemo, and cwltool - and they all appear to just consume the dependency manager self.dependency_manager.dependency_shell_commands interface and not use shell_commands directly. This looks good to me!

@jmchilton jmchilton merged commit 83eefb6 into galaxyproject:dev Nov 6, 2017

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@nsoranzo nsoranzo deleted the nsoranzo:refactor_shell_commands branch Nov 7, 2017

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