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Prefer versioned Conda dependencies to unversioned Galaxy ones #3708

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merged 2 commits into from Mar 10, 2017

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commented Mar 3, 2017

We have been trying to get the updated dunovo tools working on Main and ran into both an install time and run time problem of the bowtie2 dependency, which was specified as 2.2.5, resolving via Galaxy packages as 2.1.0. This is due to us having a default symlink to 2.1.0 from Way Back In The Day before they were handled by TS dependencies. Ultimately we don't have any unversioned requirement tags that depend on it, so I removed the default symlink.

I can't imagine any situation in which you'd want an unversioned dependency over a versioned one, even in the explicit "I am making a decision as an admin to override the conda version" case - just use the versioned Galaxy dep in that case. If you really do want unversioned Galaxy deps to override versioned Conda deps then set up a dependency resolvers conf accordingly.

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commented Mar 3, 2017

That said, @jmchilton insists I argued for it to be the way it is now. I can't remember why I would have argued for it or whether I had a technical argument for it, though.

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commented Mar 3, 2017

The docs are incorrect throughout now though.

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commented Mar 3, 2017

Ah, we should definitely fix that before merging this if we decide we want to make this change.

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commented Mar 3, 2017

I had the same issue with a bunch of dependencies, ended up removing many default symlinks. 👍

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commented Mar 10, 2017

+1, thanks for updating the docs.

@dannon dannon merged commit 33ff275 into galaxyproject:dev Mar 10, 2017

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jmchilton added a commit to galaxyproject/galaxy-lib that referenced this pull request Mar 11, 2017

@natefoo natefoo deleted the natefoo:dep-resolve-order branch Mar 29, 2017

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