Add seqrepo and vrs-python docker scripts and github action

.github/workflows/build-seqrepo-slim.yaml

@@ -0,0 +1,89 @@
+name: Build SeqRepo Slim Container
+
+on:
+  release:
+    types: [published]
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}/seqrepo-slim
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    strategy:
+      matrix:
+        assembly: [GRCh38, GRCh37]
+
+    env:
+      ASSEMBLY: ${{ matrix.assembly }}
+      BASE_TAG: ghcr.io/${{ github.repository }}/seqrepo-slim
+
+    steps:
+    - name: Checkout vrs-python repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+      with:
+        driver-opts: |
+          image=moby/buildkit:latest
+
+    - name: Log in to Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Build and push data stage
+      uses: docker/build-push-action@v5
+      with:
+        context: misc/containers
+        file: misc/containers/Dockerfile
+        platforms: linux/amd64,linux/arm64
+        target: data
+        build-args: |
+          ASSEMBLY=${{ env.ASSEMBLY }}
+        cache-from: type=registry,ref=${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}-data
+        tags: ${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}-data
+        push: true
+
+    - name: Build and push build stage
+      uses: docker/build-push-action@v5
+      with:
+        context: misc/containers
+        file: misc/containers/Dockerfile
+        platforms: linux/amd64,linux/arm64
+        target: build
+        build-args: |
+          ASSEMBLY=${{ env.ASSEMBLY }}
+        cache-from: |
+          type=registry,ref=${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}-data
+          type=registry,ref=${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}-build
+        tags: ${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}-build
+        push: true
+
+    - name: Build and push final stage
+      uses: docker/build-push-action@v5
+      with:
+        context: misc/containers
+        file: misc/containers/Dockerfile
+        platforms: linux/amd64,linux/arm64
+        target: vrs-python
+        build-args: |
+          ASSEMBLY=${{ env.ASSEMBLY }}
+        cache-from: |
+          type=registry,ref=${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}-data
+          type=registry,ref=${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}-build
+          type=registry,ref=${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}
+        tags: |
+          ${{ env.BASE_TAG }}:${{ env.ASSEMBLY }}
+          ${{ env.BASE_TAG }}:latest
+        push: true

docker-compose.yml

@@ -26,7 +26,7 @@ services:
     volumes:
       - uta_vol:/var/lib/postgresql/data
     ports:
-      - 5432:5432
+      - 5433:5432
 
 volumes:
   seqrepo_vol:

misc/containers/Dockerfile

@@ -0,0 +1,91 @@
+###
+# podman build --arch linux/amd64,linux/arm64 --build-arg ASSEMBLY=GRCh38 -t docker.io/ga4gh/vrs-python:GRCh38 -f ./Dockerfile .
+# podman build --arch linux/arm64 --build-arg ASSEMBLY=GRCh38 --target build -t docker.io/ga4gh/vrs-python:GRCh38-build -f ./Dockerfile .
+###
+# Data layer - downloads genomic reference files
+FROM python:3.12-slim AS data
+
+# Either 'GRCh38' or 'GRCh37'
+ARG ASSEMBLY="GRCh38"
+
+# Tell build-seqrepo where to put the data
+ENV SEQREPO_ROOT_DIR=/seqrepo-${ASSEMBLY}
+
+# Install curl for downloading
+RUN apt-get update && apt-get install -y curl \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /data
+
+# Download the appropriate genomic reference file based on assembly
+COPY build-${ASSEMBLY}.bash /data/
+RUN . /data/build-${ASSEMBLY}.bash \
+    && download_reference
+
+# Builder image
+FROM python:3.12-slim AS build
+
+# Either 'GRCh38' or 'GRCh37'
+ARG ASSEMBLY="GRCh38"
+
+# Install packages needed for the build
+RUN apt-get update && apt-get upgrade -y && apt-get install -y \
+    curl \
+    git \
+    libpq-dev \
+    python3-pip \
+    python3-venv \
+    tabix \
+    rsync \
+    zlib1g-dev \
+    postgresql-client \
+    unzip \
+    libhts3 \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /vrs-python
+
+# Copy downloaded genomic files from data layer
+COPY --from=data /data/* /data/
+
+# Setup the virtual env for vrs-python
+RUN python3 -m venv /vrs-python/venv
+ENV PATH=/vrs-python/venv/bin:$PATH
+
+# Tell build-seqrepo where to put the data
+ENV SEQREPO_ROOT_DIR=/seqrepo-${ASSEMBLY}
+
+# Install vrs-python
+RUN /vrs-python/venv/bin/python3 -m pip install -U setuptools 'ga4gh.vrs[extras]' biocommons.seqrepo
+
+# Build the seqrepo data using provided function
+COPY build-${ASSEMBLY}.bash /tmp/build-${ASSEMBLY}.bash
+RUN cd /data && . /tmp/build-${ASSEMBLY}.bash \
+    && build_seqrepo
+
+# Final image
+FROM python:3.12-slim AS vrs-python
+ARG ASSEMBLY="GRCh38"
+ENV ASSEMBLY=${ASSEMBLY}
+
+# Install runtime required packages
+RUN apt-get update && apt-get install -y libpq-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy over artifacts from the builder
+COPY --from=build /vrs-python /vrs-python
+COPY --from=build /seqrepo-${ASSEMBLY} /seqrepo-${ASSEMBLY}
+
+# Copy over run script
+COPY ./entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+
+# Set environment variables
+ENV GA4GH_VRS_DATAPROXY_URI="seqrepo+file:///seqrepo-${ASSEMBLY}/master"
+ENV SEQREPO_ROOT_DIR=/seqrepo-${ASSEMBLY}
+ENV VIRTUAL_ENV=/vrs-python/venv
+ENV PATH=/vrs-python/venv/bin:$PATH
+
+WORKDIR /
+
+ENTRYPOINT [ "/entrypoint.sh" ]

misc/containers/build-GRCh37.bash

@@ -0,0 +1,23 @@
+#!/bin/bash
+set -xeuo pipefail
+
+if [ -z $SEQREPO_ROOT_DIR ]; then
+    echo "Must set SEQREPO_ROOT_DIR"
+    exit 1
+fi
+
+reference_url=https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.13_GRCh37/GCF_000001405.13_GRCh37_genomic.fna.gz
+reference_fname=$(basename $reference_url)
+
+download_reference() {
+    curl -O $reference_url
+    echo "$reference_url"
+}
+
+build_seqrepo() {
+    # Load reference genome from pre-downloaded file
+    # File should already be present from Docker data layer
+    seqrepo -r $SEQREPO_ROOT_DIR init
+    seqrepo -r $SEQREPO_ROOT_DIR load -n NCBI $reference_fname
+    seqrepo -r $SEQREPO_ROOT_DIR add-assembly-names
+}

misc/containers/build-GRCh38.bash

@@ -0,0 +1,25 @@
+#!/bin/bash
+set -xeuo pipefail
+
+if [ -z $SEQREPO_ROOT_DIR ]; then
+    echo "Must set SEQREPO_ROOT_DIR"
+    exit 1
+fi
+
+reference_url=https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.26_GRCh38/GCF_000001405.26_GRCh38_genomic.fna.gz
+reference_fname=$(basename $reference_url)
+
+echo "PATH: $PATH"
+
+download_reference() {
+    curl -O $reference_url
+    echo "$reference_url"
+}
+
+build_seqrepo() {
+    # Load reference genome from pre-downloaded file
+    # File should already be present from Docker data layer
+    seqrepo -r $SEQREPO_ROOT_DIR init
+    seqrepo -r $SEQREPO_ROOT_DIR load -n NCBI $reference_fname
+    seqrepo -r $SEQREPO_ROOT_DIR add-assembly-names
+}

misc/containers/build-with-tar.sh

@@ -0,0 +1,76 @@
+#!/bin/bash
+
+# Build script that creates a tar.gz with only necessary files for container build
+# Usage: ./build-with-tar.sh [ASSEMBLY]
+
+set -e
+
+ASSEMBLY=${1:-GRCh38}
+TAR_NAME="build-context.tar.gz"
+BUILD_DIR="build-context"
+
+echo "Building container with assembly: $ASSEMBLY"
+echo "Creating build context tar.gz..."
+
+# Clean up any existing build context
+rm -rf "$BUILD_DIR" "$TAR_NAME"
+
+# Create build directory
+mkdir -p "$BUILD_DIR/misc/containers"
+
+# Copy necessary files for the container build
+echo "Copying files to build context..."
+
+# Container-specific files
+cp misc/containers/Dockerfile "$BUILD_DIR/misc/containers/"
+cp misc/containers/entrypoint.sh "$BUILD_DIR/misc/containers/"
+cp misc/containers/build-${ASSEMBLY}.bash "$BUILD_DIR/misc/containers/"
+
+# Create the tar.gz
+echo "Creating tar.gz..."
+rm -rf "$TAR_NAME"
+tar -czf "$TAR_NAME" -C "$BUILD_DIR" .
+
+# Clean up build directory
+rm -rf "$BUILD_DIR"
+
+echo "Build context created: $TAR_NAME"
+
+# Detect container runtime
+if command -v docker >/dev/null 2>&1; then
+    CONTAINER_CMD="docker"
+    echo "Using Docker for build..."
+elif command -v podman >/dev/null 2>&1; then
+    CONTAINER_CMD="podman"
+    echo "Using Podman for build..."
+else
+    echo "Error: Neither docker nor podman found in PATH"
+    exit 1
+fi
+
+# Run container build with the tar.gz as context
+cat "$TAR_NAME" | $CONTAINER_CMD build \
+    --arch linux/arm64,linux/amd64 \
+    --build-arg ASSEMBLY="$ASSEMBLY" \
+    --target data \
+    -t ghcr.io/theferrit32/vrs-python:${ASSEMBLY}-data \
+    -f ./misc/containers/Dockerfile
+
+cat "$TAR_NAME" | $CONTAINER_CMD build \
+    --arch linux/arm64,linux/amd64 \
+    --build-arg ASSEMBLY="$ASSEMBLY" \
+    --target build \
+    -t ghcr.io/theferrit32/vrs-python:${ASSEMBLY}-build \
+    -f ./misc/containers/Dockerfile
+
+cat "$TAR_NAME" | $CONTAINER_CMD build \
+    --arch linux/arm64,linux/amd64 \
+    --build-arg ASSEMBLY="$ASSEMBLY" \
+    --target build \
+    -t ghcr.io/theferrit32/vrs-python:${ASSEMBLY} \
+    -f ./misc/containers/Dockerfile
+
+# Clean up tar file
+# rm -f "$TAR_NAME"
+
+echo "Build completed successfully!"

misc/containers/entrypoint.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+/vrs-python/venv/bin/vrs-annotate vcf --assembly ${ASSEMBLY} $@