Add $GALAXY_SLOTS and $GALAXY_MEMORY_MB to bbmerge
#5937
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bgruening
approved these changes
Apr 9, 2024
| @@ -39,7 +39,12 @@ | |||
| ln -s '${read2}' '${read2_file}' && | |||
| #end if | |||
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| bbmerge.sh | |||
| if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then | |||
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I'm a bit scared of the unquoted * characters.
If we use the same code in different tools we should use a macro token.
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This is in a bash double bracket evaluation which I believe is safe (patterns are not matched)?
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shellcheck also does not complain. should be fine.
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Worth noting that setting
-Xmxvia$_JAVA_OPTIONSin the job env as many admins do still overrides this. I pulled the clever bit of handling for that from bbnorm.FOR CONTRIBUTOR: