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All tools can have _JAVA_OPTIONS #2363

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cat-bro
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@cat-bro cat-bro commented Jan 30, 2025

a bunch of pilon jobs failed because the tool had the _JAVA_OPTIONS environment variable but not the SINGULARITYENV__JAVA_OPTIONS environment variable.

All tools can have java options set - they won't be used if it's not a java tool anyway. The lack of propagation of regular environment variables for container jobs is annoying but easy enough to get around if the variable can be put on the default tool like this.

@cat-bro cat-bro requested a review from jlqfab January 30, 2025 06:15
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Looks good!

@jlqfab jlqfab merged commit ad03154 into usegalaxy-au:master Jan 30, 2025
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jlqfab commented Jan 30, 2025

Actually, just realised this will set -Xmx to the default memory, won't it?

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2 participants