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Added a check for whether files can be created and executed within the configured tmp-dir #8951

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@KevinCLydon KevinCLydon commented Aug 13, 2024

Adds a couple warnings in case the user can write to the configured tmp-dir but can't set the files as executable or execute them, with the assumption in the latter case that the cause is likely that the directory is mounted using the "noexec" mount option.

I'm not sure if a test makes sense for this, because it would probably require mounting a directory for testing, and the user running the tests may not have permissions to do that. I think only root can mount with options in Ubuntu? Do we require root for other tests?

Fixes #8453

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gatk-bot commented Aug 13, 2024

Github actions tests reported job failures from actions build 10373907397
Failures in the following jobs:

Test Type JDK Job ID Logs
integration 17.0.6+10 10373907397.11 logs
integration 17.0.6+10 10373907397.0 logs

@jamesemery jamesemery self-assigned this Sep 23, 2024
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GATK should warn the user when the temp dir is "noexec"
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