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Remove AUGUR_RECURSION_LIMIT #115

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merged 1 commit into from
Aug 11, 2023
Merged

Remove AUGUR_RECURSION_LIMIT #115

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4 changes: 0 additions & 4 deletions Snakefile
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Expand Up @@ -2,10 +2,6 @@ import datetime
import pandas as pd
from treetime.utils import numeric_date

# Set the maximum recursion limit globally for all shell commands, to avoid
# issues with large trees crashing the workflow. Preserve Snakemake's default
# use of Bash's "strict mode", as we rely on that behaviour.
shell.prefix("set -euo pipefail; export AUGUR_RECURSION_LIMIT=10000; ")

wildcard_constraints:
segment = r'pb2|pb1|pa|ha|np|na|ma',
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3 changes: 0 additions & 3 deletions profiles/scicore/submit.sh
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Expand Up @@ -8,8 +8,5 @@ source ~/miniconda3/etc/profile.d/conda.sh
conda activate nextstrain
#Test
export AUGUR_MINIFY_JSON=1
export AUGUR_RECURSION_LIMIT=10000

{exec_job}