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Improve default handling of Singularity volumes. #4180

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merged 2 commits into from Jun 12, 2017

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commented Jun 12, 2017

My understanding is that unlike Docker, Singularity doesn't allow a subdirectory to be mounted rw and its parent to be mounted ro - it will just be ro. This PR adjusts the default volume handling for Singularity to intelligently fallback to mounting parent directories as rw if their child directories are listed as being mounted rw.

Ping @bgruening - is the above a description correct and does this approach work for you?

xref #4175

Improve default handling of Singularity volumes.
My understanding is that unlike Docker, Singularity doesn't allow a subdirectory to be mounted rw and its parent to be mounted ro - it will just be ro. This PR adjusts the default volume handling for Singularity to intelligently fallback to mounting parent directories as rw if their child directories are listed as being mounted rw.

Ping @bgruening - is the above a description correct and does this approach work for you?
(this is known as the job directory) as ro and the working directory itself as rw.
This doesn't work in Singularity because if any parent directory is mounted as ro
none of its children will be rw. So the job directory will be mounted rw for
Singularity.

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@bgruening

bgruening Jun 12, 2017

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We should add what $defaults means in the singularity context by default.

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@jmchilton

jmchilton Jun 12, 2017

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It is the same as Docker though. Do you want me to duplicate the text down here or are you saying I should state what the paths would be on a fresh default install or something else?

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@bgruening

bgruening Jun 12, 2017

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You are right, people should just read the text above - don't copy it.

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commented Jun 12, 2017

The failing test is unrelated. Thanks @jmchilton!

@bgruening bgruening merged commit f81c5bb into galaxyproject:dev Jun 12, 2017

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jmchilton added a commit to jmchilton/galaxy that referenced this pull request Jun 20, 2017

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