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Update AWS CLI to v2 #287

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Merged
joverlee521 merged 1 commit into from
Jun 24, 2026
+13 −12
Merged

Update AWS CLI to v2 #287

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21 changes: 11 additions & 10 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ COPY --from=xx / /
# make: used for building from Makefiles (search for usage); may be used by package managers to build from source
# nodejs: for installing Auspice
# clang: for compiling C/C++ projects; may be used by package managers to build from source
# unzip: for AWS CLI
RUN apt-get update && apt-get install -y --no-install-recommends \
autoconf \
automake \
Expand All @@ -36,7 +37,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
curl \
git \
make \
dpkg-dev
dpkg-dev \
unzip

# Install a specific Node.js version
# https://github.com/nodesource/distributions/blob/ba48c1fe6e843e9ffb60aefc5da5d00234c83f04/README.md#using-debian-as-root-nodejs-20
Expand Down Expand Up @@ -208,6 +210,14 @@ RUN curl -fsSL https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-$
RUN curl -fsSL https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-${TARGETARCH}/dataformat \
-o /final/bin/dataformat

# Install tooling for our AWS Batch builds, which use `aws s3`.
# Using `xx-info march` to translate amd64 -> x86_64 and arm64 -> aarch64
# based on https://github.com/docker/buildx/discussions/2001
Comment on lines +214 to +215

@victorlin victorlin Jun 22, 2026

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Nice find, this can probably replace builder-scripts/target-triple elsewhere.

RUN XX_MARCH=$(xx-info march) \
&& curl -fsSL --proto '=https' "https://awscli.amazonaws.com/awscli-exe-linux-${XX_MARCH}.zip" -o "awscliv2.zip" \

@victorlin victorlin Jun 22, 2026

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We have also been using awscli >= 2 in conda-base without any issues.

I'm guessing there's a good amount of AWS CLI usage not captured by pathogen repo CI (e.g. upload-to-s3), but we can just merge and monitor.

@joverlee521 joverlee521 Jun 24, 2026

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No obvious errors in today's pathogen workflows, will continue to monitor the rest of the week.

&& unzip awscliv2.zip "aws/dist/*" -d /final/libexec/aws-cli \
&& ln -srv /final/libexec/aws-cli/aws/dist/aws /final/bin/aws

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

# Define a builder stage that runs on the target platform.
Expand Down Expand Up @@ -244,11 +254,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
# Install envdir, which is used by pathogen builds
RUN pip3 install envdir==1.0.1

# Install tooling for our AWS Batch builds, which use `aws s3`.
RUN python3 -m venv /usr/local/libexec/awscli \
&& /usr/local/libexec/awscli/bin/python -m pip install awscli==1.18.195 \
&& ln -sv /usr/local/libexec/awscli/bin/aws /usr/local/bin/aws

# Install Snakemake and related optional dependencies.
# Pinned to 9.6.2 for stability (latest version on 2025-07-03)
RUN pip3 install snakemake[reports]==9.6.2
Expand Down Expand Up @@ -388,9 +393,6 @@ RUN chmod a+rx /usr/local/bin/* /usr/local/libexec/*
# Add installed Python libs
COPY --from=builder-target-platform /usr/local/lib/python3.11/site-packages/ /usr/local/lib/python3.11/site-packages/

# AWS CLI
COPY --from=builder-target-platform /usr/local/libexec/awscli/ /usr/local/libexec/awscli/

# Add installed Python scripts that we need.
#
# XXX TODO: This isn't great. It's prone to needing manual updates because it
Expand All @@ -402,7 +404,6 @@ COPY --from=builder-target-platform /usr/local/libexec/awscli/ /usr/local/libexe
# -trs, 15 June 2018
COPY --from=builder-target-platform \
/usr/local/bin/augur \
/usr/local/bin/aws \
/usr/local/bin/bio \
/usr/local/bin/envdir \
/usr/local/bin/evofr \
Expand Down
4 changes: 2 additions & 2 deletions tests/envdir-url.t
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Expand Up @@ -24,7 +24,7 @@ Files are populated from NEXTSTRAIN_ENVD_URL.

$ aws s3 cp --quiet env.d.zip "$NEXTSTRAIN_ENVD_URL"

$ docker run --rm -e NEXTSTRAIN_ENVD_URL --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN} "$IMAGE" \
$ docker run --rm -e NEXTSTRAIN_ENVD_URL --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN,DEFAULT_REGION} "$IMAGE" \
> bash -eu -c 'echo "$a"; echo "$b"'
download: s3://nextstrain-tmp/*.zip to ../env.d.zip (glob)
Archive: /nextstrain/env.d.zip
Expand All @@ -37,7 +37,7 @@ Files are populated from NEXTSTRAIN_ENVD_URL.

Files and NEXTSTRAIN_ENVD_URL are removed with NEXTSTRAIN_DELETE_ENVD=1.

$ docker run --rm -e NEXTSTRAIN_DELETE_ENVD=1 -e NEXTSTRAIN_ENVD_URL --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN} "$IMAGE" \
$ docker run --rm -e NEXTSTRAIN_DELETE_ENVD=1 -e NEXTSTRAIN_ENVD_URL --env=AWS_{ACCESS_KEY_ID,SECRET_ACCESS_KEY,SESSION_TOKEN,DEFAULT_REGION} "$IMAGE" \
> bash -eu -c 'echo "$a"; echo "$b"; ls -1 /nextstrain/env.d'
download: s3://nextstrain-tmp/*.zip to ../env.d.zip (glob)
Archive: /nextstrain/env.d.zip
Expand Down
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