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Remove AUGUR_RECURSION_LIMIT #1080

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Aug 11, 2023
Merged

Remove AUGUR_RECURSION_LIMIT #1080

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4 changes: 0 additions & 4 deletions Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,6 @@ from collections import OrderedDict
import textwrap
import time

# 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; ")

# Store the user's configuration prior to loading defaults, so we can check for
# reused subsampling scheme names in the user's config. We need to make a deep
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5 changes: 1 addition & 4 deletions nextstrain_profiles/nextstrain-scicore/submit.sh
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@@ -1,14 +1,11 @@
#!/bin/sh

#SBATCH --output=log/%j.out # where to store the output ( %j is the JOBID )
#SBATCH --error=log/%j.err # where to store error messages

# activate conda environment
source /scicore/home/neher/neher/miniconda3/etc/profile.d/conda.sh
conda activate nextstrain
export AUGUR_MINIFY_JSON=1
export AUGUR_RECURSION_LIMIT=10000

{exec_job}