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prefer VEP_CONFIG_URI access inside hail itself
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v03_pipeline/lib/vep.py

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Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@ def run_vep(
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validate_vep_config_reference_genome(reference_genome)
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return hl.vep(
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ht,
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config=os.environ['VEP_CONFIG_URI'],
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# We set no config option here to instead use the `VEP_CONFIG_URI` environment variable.
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name='vep',
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block_size=1000,
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tolerate_parse_error=True,

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