Set global recursion limit for shell commands #690
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Instead of setting the recursion limit for individual rules as issues with maximum recursion occur, we set the recursion limit as an environment variable prefixed to all shell commands in the workflow. This approach allows us to control the limit with a single variable and affect the entire workflow. Resolves #689
jameshadfield
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Jul 26, 2021
joverlee521
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Apr 14, 2023
We've had to use the `AUGUR_RECURSION_LIMIT` environment variable to bump the recursion limit for SARS-CoV-2 builds¹, mpox builds², and our `nextstrain-jobs` definition in AWS Batch. From a general search of the envvar across GitHub³, 10,000 looks like the default that others use as well (although this may be influenced by our discussions⁴). ¹ nextstrain/ncov#690 ² nextstrain/mpox#150 ³ https://cs.github.com/?scopeName=All+repos&scope=&q=AUGUR_RECURSION_LIMIT%3D ⁴ #328
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joverlee521
added a commit
to nextstrain/augur
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Apr 17, 2023
We've had to use the `AUGUR_RECURSION_LIMIT` environment variable to bump the recursion limit for SARS-CoV-2 builds¹, mpox builds², and our `nextstrain-jobs` definition in AWS Batch. From a general search of the envvar across GitHub³, 10,000 looks like the default that others use as well (although this may be influenced by our discussions⁴). ¹ nextstrain/ncov#690 ² nextstrain/mpox#150 ³ https://cs.github.com/?scopeName=All+repos&scope=&q=AUGUR_RECURSION_LIMIT%3D ⁴ #328
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Description of proposed changes
Instead of setting the recursion limit for individual rules as issues with maximum recursion occur, we set the recursion limit as an environment variable prefixed to all shell commands in the workflow. This approach allows us to control the limit with a single variable and affect the entire workflow.
Related issue(s)
Fixes #689
Testing
Release checklist
This is a minor change.