Snakefile: Set AUGUR_RECURSION_LIMIT=10000 #150
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This change is a response to the recursion error that a user ran into when running the workflow with a large number of sequences during Nextstrain office hours on 2023-04-13. Set the recursion limit globally instead of asking the user to remember to set the environment variable or edit their own Snakefile.
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We've never seen this issue with the Nextstrain automated builds in AWS Batch because the |
tsibley
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Apr 14, 2023
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
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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
This change is a response to the recursion error that a user ran into when running the workflow with a large number of sequences during Nextstrain office hours on 2023-04-13.
Set the recursion limit globally instead of asking the user to remember to set the environment variable or edit their own Snakefile.
Testing