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dpark01claude
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Revert snpeff to >=4.3.1t to fix ARM64 solver conflict
The snpeff=5.2 pin (and its openjdk>=11 dep) creates an unsolvable icu version conflict on ARM64 with fgbio's r-base, vphaser2's boost-cpp, and csvkit's pyicu. Reverting to unblock builds while we investigate alternative approaches to address snpeff's Log4Shell CVE. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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docker/requirements/phylo.txt

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@@ -4,5 +4,5 @@ lofreq>=2.1.5
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mafft>=7.508
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mummer4>=4.0.0rc1
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muscle=3.8.1551
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snpeff=5.2
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snpeff>=4.3.1t
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vphaser2>=2.0

src/viral_ngs/phylo/snpeff.py

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@@ -23,7 +23,7 @@
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_log = logging.getLogger(__name__)
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TOOL_NAME = 'snpEff'
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TOOL_VERSION = '5.2'
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TOOL_VERSION = '4.3.1t'
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class SnpEff(core.Tool):

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