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Install pathogen-embed and evofr together #296

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Merged
joverlee521 merged 1 commit into from
Aug 14, 2026
Merged

Install pathogen-embed and evofr together #296

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7 changes: 3 additions & 4 deletions Dockerfile
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Expand Up @@ -283,7 +283,9 @@ RUN pip3 install epiweeks==2.1.2
# Install pango_aliasor (for forecasts-ncov)
RUN pip3 install pango_aliasor==0.3.0

RUN pip3 install pathogen-embed==3.0.0
# Install pathogen-embed and evofr together for proper dependency resolution of numpy.
# They can be separated when pathogen-embed unpins numba/numpy.
RUN pip3 install pathogen-embed==3.0.0 evofr
RUN pip3 install xlrd==2.0.1

# Install openpyxl for pandas in GenoFLU
Expand Down Expand Up @@ -329,9 +331,6 @@ WORKDIR /nextstrain/augur
RUN /builder-scripts/download-repo https://github.com/nextstrain/augur "$(/builder-scripts/latest-augur-release-tag)" . \
&& pip3 install --editable .

# Add evofr for forecasting
RUN pip3 install evofr

# ———————————————————————————————————————————————————————————————————— #

# Now build the final image.
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