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Building docker images for both architectures
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‎docker/README.md‎

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@@ -14,21 +14,58 @@ docker pull ghcr.io/openmined/bioscript:0.1.0
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Images are automatically built and pushed on every commit to main and on releases.
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## Building Locally
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## Building
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### Local (single architecture)
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From the repository root:
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```bash
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docker build -f docker/Dockerfile -t bioscript:0.1.0 .
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```
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Or use the build script:
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### Multi-architecture (amd64 + arm64)
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The build script runs Docker Buildx once to generate a multi-architecture manifest for both `linux/amd64` and `linux/arm64`.
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```bash
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./docker/build.sh 0.1.0
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```
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By default the manifest is pushed to GitHub Container Registry. Switch to a local OCI archive by setting `OUTPUT_MODE=oci` (the archive is written to `docker/dist/bioscript-<version>.oci.tar` unless `OUTPUT_DEST` is provided):
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```bash
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OUTPUT_MODE=oci ./docker/build.sh 0.1.0
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```
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After building you can inspect the manifest to confirm both platforms are present:
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```bash
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cd docker
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./build.sh
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docker buildx imagetools inspect ghcr.io/openmined/bioscript:0.1.0
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```
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Environment knobs:
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- `OUTPUT_MODE=push|oci` (default `push`)
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- `OUTPUT_DEST=path/to/archive.tar` when `OUTPUT_MODE=oci`
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- `LOAD_PLATFORM=linux/amd64|linux/arm64|none` (default `auto`, meaning match the host). The script always executes the multi-arch build first, then optionally loads one platform locally for quick testing.
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> **Note:** Run `docker login ghcr.io` before using `OUTPUT_MODE=push`.
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### Local architecture-specific tests
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To build and exercise the container for a single architecture without pushing to GHCR, use the helper scripts in the repository root:
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```bash
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# On x86_64 hosts
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./test_docker_amd64.sh
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# On arm64 hosts (including Apple Silicon)
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./test_docker_arm64.sh
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```
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These scripts perform the multi-arch build, load the host architecture locally, and exercise the classifier with `docker run --platform=<arch> ...`.
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## Usage
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### Run a classifier

‎docker/build.sh‎

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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#!/bin/bash
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set -e
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set -euo pipefail
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# Build BioScript Docker image
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#
@@ -10,27 +10,136 @@ set -e
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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cd "$SCRIPT_DIR/.."
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PLATFORMS=${PLATFORMS:-linux/amd64,linux/arm64}
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BUILDER_NAME=${BUILDER_NAME:-bioscript-builder}
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REMOTE_IMAGE=${REMOTE_IMAGE:-ghcr.io/openmined/bioscript}
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OUTPUT_MODE=${OUTPUT_MODE:-push} # push|oci
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OUTPUT_DEST="${OUTPUT_DEST:-}"
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LOAD_PLATFORM=${LOAD_PLATFORM:-auto} # auto|none|<platform>
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VERIFY_MANIFEST=${VERIFY_MANIFEST:-0}
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# Get version from argument or __init__.py
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if [ -n "$1" ]; then
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if [ -n "${1:-}" ]; then
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VERSION="$1"
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else
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VERSION=$(grep '^__version__ = ' python/src/bioscript/__init__.py | cut -d'"' -f2)
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fi
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echo "Building bioscript:${VERSION}..."
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if [ -z "$OUTPUT_DEST" ]; then
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OUTPUT_DEST="docker/dist/bioscript-${VERSION}.oci.tar"
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fi
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if ! docker buildx inspect "$BUILDER_NAME" >/dev/null 2>&1; then
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echo "Creating docker buildx builder '$BUILDER_NAME'..."
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docker buildx create --name "$BUILDER_NAME" --driver docker-container >/dev/null
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fi
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docker buildx use "$BUILDER_NAME" >/dev/null
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docker buildx inspect "$BUILDER_NAME" --bootstrap >/dev/null
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echo "Building bioscript:${VERSION} for ${PLATFORMS}..."
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REMOTE_TAGS=( )
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if [ -n "$REMOTE_IMAGE" ]; then
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REMOTE_TAGS=("${REMOTE_IMAGE}:${VERSION}" "${REMOTE_IMAGE}:latest")
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fi
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BUILD_CMD=(docker buildx build
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--builder "$BUILDER_NAME"
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--platform "$PLATFORMS"
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-f docker/Dockerfile
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)
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for tag in "${REMOTE_TAGS[@]}"; do
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BUILD_CMD+=( -t "$tag" )
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done
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case "$OUTPUT_MODE" in
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push)
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if [ "${#REMOTE_TAGS[@]}" -eq 0 ]; then
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echo "REMOTE_IMAGE must be set when OUTPUT_MODE=push" >&2
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exit 1
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fi
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BUILD_CMD+=( --push )
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;;
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oci)
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mkdir -p "$(dirname "$OUTPUT_DEST")"
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BUILD_CMD+=( --output "type=oci,dest=${OUTPUT_DEST}" )
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;;
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*)
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echo "Unsupported OUTPUT_MODE: $OUTPUT_MODE" >&2
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exit 1
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;;
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esac
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BUILD_CMD+=( . )
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"${BUILD_CMD[@]}"
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docker build \
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-f docker/Dockerfile \
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-t "bioscript:${VERSION}" \
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-t "bioscript:latest" \
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-t "ghcr.io/openmined/bioscript:${VERSION}" \
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-t "ghcr.io/openmined/bioscript:latest" \
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.
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LOAD_PLATFORM_RESOLVED=""
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if [ "$LOAD_PLATFORM" = "auto" ]; then
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case "$(uname -m)" in
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x86_64)
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LOAD_PLATFORM_RESOLVED="linux/amd64"
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;;
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arm64|aarch64)
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LOAD_PLATFORM_RESOLVED="linux/arm64"
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;;
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*)
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echo "Skipping local load: unsupported host architecture '$(uname -m)'" >&2
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LOAD_PLATFORM_RESOLVED=""
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;;
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esac
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elif [ "$LOAD_PLATFORM" = "none" ]; then
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LOAD_PLATFORM_RESOLVED=""
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else
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LOAD_PLATFORM_RESOLVED="$LOAD_PLATFORM"
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fi
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LOCAL_TAGS=("bioscript:${VERSION}" "bioscript:latest")
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LOCAL_LOADED=0
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if [ -n "$LOAD_PLATFORM_RESOLVED" ]; then
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LOAD_CMD=(docker buildx build
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--builder "$BUILDER_NAME"
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--platform "$LOAD_PLATFORM_RESOLVED"
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-f docker/Dockerfile
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)
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for tag in "${LOCAL_TAGS[@]}"; do
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LOAD_CMD+=( -t "$tag" )
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done
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LOAD_CMD+=( --load . )
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"${LOAD_CMD[@]}"
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LOCAL_LOADED=1
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fi
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echo "✓ Built bioscript:${VERSION}"
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echo " Tagged: bioscript:${VERSION}, bioscript:latest"
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echo " Tagged: ghcr.io/openmined/bioscript:${VERSION}, ghcr.io/openmined/bioscript:latest"
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case "$OUTPUT_MODE" in
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push)
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echo " Multi-arch pushed: ${REMOTE_TAGS[*]}"
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;;
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oci)
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echo " Multi-arch OCI archive: ${OUTPUT_DEST}"
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;;
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esac
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if [ "$LOCAL_LOADED" = "1" ]; then
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echo " Loaded local image for ${LOAD_PLATFORM_RESOLVED}: bioscript:${VERSION}, bioscript:latest"
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else
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echo " Local image not loaded"
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fi
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if [ "$VERIFY_MANIFEST" = "1" ]; then
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if [ "$OUTPUT_MODE" = "push" ]; then
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docker buildx imagetools inspect "${REMOTE_IMAGE}:${VERSION}"
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else
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echo "(Skipping manifest inspect: only available for pushed images)"
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fi
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fi
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echo ""
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echo "Test with:"
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echo " docker run --rm bioscript:${VERSION}"
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echo " docker run --rm ghcr.io/openmined/bioscript:latest"
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echo "Suggested next steps:"
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if [ "$OUTPUT_MODE" = "push" ]; then
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echo " docker buildx imagetools inspect ${REMOTE_IMAGE}:${VERSION}"
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fi
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if [ "$LOCAL_LOADED" = "1" ]; then
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echo " docker run --platform=${LOAD_PLATFORM_RESOLVED} --rm bioscript:${VERSION}"
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fi

‎test_docker.sh‎

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#!/bin/bash
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set -e
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set -euo pipefail
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# Test bioscript using Docker
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# Rebuilds the container and runs the classifier
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REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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HOST_ARCH=$(uname -m)
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case "$HOST_ARCH" in
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x86_64)
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DEFAULT_PLATFORM="linux/amd64"
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;;
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arm64|aarch64)
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DEFAULT_PLATFORM="linux/arm64"
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;;
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*)
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echo "Unsupported host architecture: $HOST_ARCH" >&2
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exit 1
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;;
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esac
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PLATFORM=${PLATFORM:-$DEFAULT_PLATFORM}
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OUTPUT_MODE=${OUTPUT_MODE:-oci}
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LOAD_PLATFORM=${LOAD_PLATFORM:-$PLATFORM}
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BUILD_PLATFORMS=${BUILD_PLATFORMS:-linux/amd64,linux/arm64}
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echo "Building Docker image..." >&2
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cd "$REPO_ROOT/docker"
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bash build.sh >&2
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PLATFORMS="$BUILD_PLATFORMS" \
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OUTPUT_MODE="$OUTPUT_MODE" \
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LOAD_PLATFORM="$LOAD_PLATFORM" \
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"$REPO_ROOT/docker/build.sh" >&2
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1334
echo "" >&2
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echo "Running classification in Docker..." >&2
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echo "" >&2
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# Run with Docker
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docker run --rm \
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--platform="$PLATFORM" \
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-v "$REPO_ROOT/examples/apol1:/data" \
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-w /data \
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bioscript:latest \

‎test_docker_amd64.sh‎

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#!/bin/bash
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set -euo pipefail
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REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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PLATFORM=linux/amd64 \
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OUTPUT_MODE="${OUTPUT_MODE:-oci}" \
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LOAD_PLATFORM=linux/amd64 \
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"$REPO_ROOT/test_docker.sh"

‎test_docker_arm64.sh‎

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#!/bin/bash
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set -euo pipefail
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REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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PLATFORM=linux/arm64 \
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OUTPUT_MODE="${OUTPUT_MODE:-oci}" \
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LOAD_PLATFORM=linux/arm64 \
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"$REPO_ROOT/test_docker.sh"

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