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/ missing in files path when testing with --install_galaxy #80

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messersc opened this Issue Feb 18, 2015 · 3 comments

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messersc commented Feb 18, 2015

I noticed a strange thing when debugging my tool.
There is a / missing, so the directory structure gets screwed up and there is unwanted behaviour like left-over tmp directories.

Example

output files:
/tmp/tmp4NvYcRfiles/000/dataset_10.dat
/tmp/tmp4NvYcRfiles/000/dataset_11.dat
current working dir:
/tmp/tmp4NvYcR/job_working_directory/000/9

where /tmp/tmp4NvYcR/galaxy-central-master/ is the tmp Galaxy root.
tmp4NvYcRfiles should (obviously?) be tmp4NvYcR/files/

Is this a bug in Galaxy or planemo?

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erasche commented Feb 18, 2015

(I'm not an official source of truth)
I've actually been using that as a feature during my test iterations--I've actually enjoyed being able to back and check the output of commands and when I have tests that fail, compare outputs. That said, you're right, it does leave an unclean /tmp/

jmchilton added a commit that referenced this issue Feb 22, 2015

Implement --no_cleanup option for test & serve commands.
Prevents deletion of temporary files created for/by Galaxy. Might be useful for debugging stuff (#80 (comment)) - probably would be a whole lot more useful for debugging if we also dropped a little shell script in that directory that allowed resuming Galaxy from that state.

@jmchilton jmchilton closed this in f3c374a Feb 22, 2015

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jmchilton commented Feb 22, 2015

@messersc thanks for the bug report, should be fixed now and I will do a new release with the fix soon.

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erasche commented Feb 22, 2015

@jmchilton thanks for adding the --no-cleanup option to support my use case :)

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