nextstrain · victorlin · Jan 7, 2026 · Nov 6, 2025 · Jan 7, 2026 · victorlin
diff --git a/.github/actions/run-integration-tests/action.yaml b/.github/actions/run-integration-tests/action.yaml
@@ -20,15 +20,18 @@ runs:
     - shell: bash -l -eo pipefail {0}
       run: nextstrain version --verbose
 
+    # Skip Docker on macOS and Windows
     - if: runner.os != 'macOS' && runner.os != 'Windows'
       shell: bash -l -eo pipefail {0}
       run: nextstrain setup docker
 
-    - if: runner.os != 'Windows'
+    # Skip Conda on Windows and Linux ARM64
+    - if: runner.os != 'Windows' && !(runner.os == 'Linux' && runner.arch == 'ARM64')
       shell: bash -l -eo pipefail {0}
       run: nextstrain setup conda
 
-    - if: runner.os != 'macOS' && runner.os != 'Windows'
+    # Skip Singularity on macOS, Windows, and Linux ARM64
+    - if: runner.os != 'macOS' && runner.os != 'Windows' && !(runner.os == 'Linux' && runner.arch == 'ARM64')
       shell: bash -l -eo pipefail {0}
       run: nextstrain setup singularity
 
@@ -38,27 +41,31 @@ runs:
     - shell: bash -l -eo pipefail {0}
       run: nextstrain version --verbose
 
+    # Skip Docker on macOS and Windows
     - if: runner.os != 'macOS' && runner.os != 'Windows'
       name: Build zika-tutorial with --docker
       shell: bash -l -eo pipefail {0}
       run: |
         git -C zika-tutorial clean -dfqx
         nextstrain build --docker --cpus 2 zika-tutorial
 
-    - if: runner.os != 'Windows'
+    # Skip Conda on Windows and Linux ARM64
+    - if: runner.os != 'Windows' && !(runner.os == 'Linux' && runner.arch == 'ARM64')
       name: Build zika-tutorial with --conda
       shell: bash -l -eo pipefail {0}
       run: |
         git -C zika-tutorial clean -dfqx
         nextstrain build --conda --cpus 2 zika-tutorial
 
-    - if: runner.os != 'macOS' && runner.os != 'Windows'
+    # Skip Singularity on macOS, Windows, and Linux ARM64
+    - if: runner.os != 'macOS' && runner.os != 'Windows' && !(runner.os == 'Linux' && runner.arch == 'ARM64')
       name: Build zika-tutorial with --singularity
       shell: bash -l -eo pipefail {0}
       run: |
         git -C zika-tutorial clean -dfqx
         nextstrain build --singularity --cpus 2 zika-tutorial
 
+    # Skip ambient on Windows
     - if: fromJSON(inputs.ambient) && runner.os != 'Windows'
       name: Build zika-tutorial with --ambient
       shell: bash -l -eo pipefail {0}

diff --git a/.github/actions/setup-integration-tests/action.yaml b/.github/actions/setup-integration-tests/action.yaml
@@ -25,6 +25,15 @@ inputs:
 runs:
   using: composite
   steps:
+    # Our aarch64 (linux/arm64) image still contains some x86_64 (amd64)
+    # executables and so requires the ability of the host to emulate x86_64.
+    # On macOS, which is the primary reason we have an aarch64 image, this is
+    # expected to be provided by Rosetta 2.  On Linux, we expect it to be QEMU,
+    # which we set up here.
+    - if: runner.os == 'Linux' && runner.arch == 'ARM64'
+      run: docker run --privileged --rm tonistiigi/binfmt --install amd64
+      shell: bash -l -eo pipefail {0}
+
     - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ inputs.python-version }}
@@ -72,14 +81,14 @@ runs:
         python3 --version | grep -F 'Python ${{ inputs.python-version }}.'
         [[ "$(python --version)" == "$(python3 --version)" ]]
 
-    # Install Singularity on Linux.
+    # Install Singularity on Linux x86_64.
     #
     # We don't install it with Conda because Conda Forge provides a non-suid
     # build of Singularity.  We're compatible with Singularity's non-suid mode,
     # but production usages of Singularity are likely to use its suid mode, so
     # I'd rather test against that.
     #   -trs, 6 Jan 2023
-    - if: runner.os == 'Linux'
+    - if: runner.os == 'Linux' && runner.arch == 'X64'
       shell: bash -l -eo pipefail {0}
       env:
         GITHUB_TOKEN: ${{ github.token }}

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -106,6 +106,10 @@ jobs:
             target: x86_64-unknown-linux-gnu
             exe: nextstrain
 
+          - os: ubuntu-22.04-arm
+            target: aarch64-unknown-linux-gnu
+            exe: nextstrain
+
           - os: macos-15-intel
             target: x86_64-apple-darwin
             exe: nextstrain
@@ -307,15 +311,17 @@ jobs:
         # fresh CI machines are not readily available, however, since
         # pre-installation is convenient for builds.
         include:
-          - { os: ubuntu-22.04,   target: x86_64-unknown-linux-gnu }
-          - { os: ubuntu-24.04,   target: x86_64-unknown-linux-gnu }
-          - { os: macos-15-intel, target: x86_64-apple-darwin }
-          - { os: macos-14,       target: x86_64-apple-darwin }
-          - { os: macos-15,       target: x86_64-apple-darwin }
-          - { os: macos-14,       target: aarch64-apple-darwin }
-          - { os: macos-15,       target: aarch64-apple-darwin }
-          - { os: windows-2022,   target: x86_64-pc-windows-msvc }
-          - { os: windows-2025,   target: x86_64-pc-windows-msvc }
+          - { os: ubuntu-22.04,     target: x86_64-unknown-linux-gnu }
+          - { os: ubuntu-24.04,     target: x86_64-unknown-linux-gnu }
+          - { os: ubuntu-22.04-arm, target: aarch64-unknown-linux-gnu }
+          - { os: ubuntu-24.04-arm, target: aarch64-unknown-linux-gnu }
+          - { os: macos-15-intel,   target: x86_64-apple-darwin }
+          - { os: macos-14,         target: x86_64-apple-darwin }
+          - { os: macos-15,         target: x86_64-apple-darwin }
+          - { os: macos-14,         target: aarch64-apple-darwin }
+          - { os: macos-15,         target: aarch64-apple-darwin }
+          - { os: windows-2022,     target: x86_64-pc-windows-msvc }
+          - { os: windows-2025,     target: x86_64-pc-windows-msvc }
 
     runs-on: ${{matrix.os}}
     defaults:
@@ -391,6 +397,10 @@ jobs:
         with:
           name: standalone-x86_64-unknown-linux-gnu
 
+      - uses: actions/download-artifact@v7
+        with:
+          name: standalone-aarch64-unknown-linux-gnu
+
       - uses: actions/download-artifact@v7
         with:
           name: standalone-x86_64-apple-darwin

diff --git a/CHANGES.md b/CHANGES.md
@@ -13,6 +13,14 @@ development source code and as such may not be routinely kept up to date.
 
 # __NEXT__
 
+## Improvements
+
+* We now produce standalone installation archives for Linux running on aarch64
+  hardware (aka arm64).  The standalone installer will use these archives
+  starting with this release.
+  ([#489](https://github.com/nextstrain/cli/pull/489),
+  [#490](https://github.com/nextstrain/cli/pull/490))
+
 ## Bug fixes
 
 * Updated the s3fs dependency to avoid versions starting with 2025.12.0. This

diff --git a/devel/pyoxidizer b/devel/pyoxidizer
@@ -27,7 +27,7 @@ main() {
             --volume "$build/cache/pyoxidizer:/tmp/.cache/pyoxidizer" \
             --volume "$build/cache/pip:/tmp/.cache/pip" \
             --volume "$build/cache/cargo:/tmp/.cargo" \
-            quay.io/pypa/manylinux2014_x86_64 "$pyoxidizer" "$@"
+            quay.io/pypa/manylinux2014_"$(platform-machine)" "$pyoxidizer" "$@"
     else
         exec "$pyoxidizer" "$@"
     fi

diff --git a/doc/changes.md b/doc/changes.md
@@ -16,6 +16,15 @@ development source code and as such may not be routinely kept up to date.
 (v-next)=
 ## __NEXT__
 
+(v-next-improvements)=
+### Improvements
+
+* We now produce standalone installation archives for Linux running on aarch64
+  hardware (aka arm64).  The standalone installer will use these archives
+  starting with this release.
+  ([#489](https://github.com/nextstrain/cli/pull/489),
+  [#490](https://github.com/nextstrain/cli/pull/490))
+
 (v-next-bug-fixes)=
 ### Bug fixes