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Update nextstrain docker image for better mpox-ing (#1704)
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vincent-czi authored Aug 27, 2024
1 parent a16a479 commit c723b60
Showing 1 changed file with 9 additions and 5 deletions.
14 changes: 9 additions & 5 deletions src/backend/Dockerfile.nextstrain
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## Dockerfile for aspen batch jobs
##
##
FROM nextstrain/base:build-20221207T221900Z
## Using most recent docker image from nextstrain's base image as of Aug 26,
## 2024 as we do work to update tree building to work correctly for mpox.
FROM nextstrain/base:build-20240822T213558Z
ARG DEBIAN_FRONTEND=noninteractive

LABEL maintainer = "CZ Gen Epi"
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RUN pip3 install nextstrain-cli csv-diff s3fs[boto3] aiobotocore[awscli,boto3] envdir fsspec pandas
RUN pip3 uninstall -y pangoLEARN

# Using most recent commit from nextstrain's ncov as of Aug 26, 2024 as we do work
# to update tree building to work correctly for mpox.
RUN mkdir /ncov && \
cd /ncov && \
git init && \
git remote add origin https://github.com/chanzuckerberg/ncov.git && \
git fetch origin czgenepi && \
git reset --hard FETCH_HEAD
git remote add origin https://github.com/nextstrain/ncov.git && \
git fetch origin master && \
git reset --hard e42576751a3e89a36d260aff70f9f6bbc62a9d32

# Add support for our custom mpox workflow
# TODO [Vincent & Dan; Aug 2024]: Update the `mpox` workflow content.
RUN mkdir /mpox && \
cd /mpox && \
git init && \
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