chore: add VEP to dev img + update base img

Dockerfile

@@ -3,6 +3,7 @@ FROM --platform=$BUILDPLATFORM debian:bullseye-slim AS downloaded-deps
 SHELL ["/bin/bash", "-c"]
 
 # Install VCF2MAF
+#  - support VEP v107+ by patching vcf2maf to remove references to removed --af_esp option
 # TODO: I don't like /opt as a home for these
 
 WORKDIR /tmp/vcf2maf
@@ -15,6 +16,7 @@ RUN apt-get update -y && \
     mv "vcf2maf-${VCF2MAF_VERSION}" vcf2maf && \
     mkdir -p /opt/data && \
     cp vcf2maf/*.pl /opt && \
+    sed -i '/ --af_esp/d' /opt/vcf2maf.pl && \
     cp -r vcf2maf/data /opt/data && \
     rm -rf vcf2maf
 
@@ -30,8 +32,8 @@ RUN curl -L \
 
 
 # Clone (but don't install yet) Ensembl-VEP
-ENV VEP_ENSEMBL_RELEASE_VERSION=111.0
-RUN git clone --depth 1 -b "release/${VEP_ENSEMBL_RELEASE_VERSION}" https://github.com/Ensembl/ensembl-vep.git && \
+ENV VEP_ENSEMBL_GIT_VERSION=111.0
+RUN git clone --depth 1 -b "release/${VEP_ENSEMBL_GIT_VERSION}" https://github.com/Ensembl/ensembl-vep.git && \
     chmod u+x ensembl-vep/*.pl
 
 # Clone ensembl-variation git repository
@@ -47,7 +49,7 @@ RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-x
 
 WORKDIR /
 
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.03.01 AS base-deps
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01 AS base-deps
 
 SHELL ["/bin/bash", "-c"]
 

dev.Dockerfile

@@ -1,4 +1,55 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.03.01 AS base-deps
+FROM --platform=$BUILDPLATFORM debian:bullseye-slim AS downloaded-deps
+
+SHELL ["/bin/bash", "-c"]
+
+# Install VCF2MAF
+#  - support VEP v107+ by patching vcf2maf to remove references to removed --af_esp option
+# TODO: I don't like /opt as a home for these
+
+WORKDIR /tmp/vcf2maf
+ENV VCF2MAF_VERSION=1.6.21
+RUN apt-get update -y && \
+    apt-get install -y curl git unzip wget && \
+    echo "https://github.com/mskcc/vcf2maf/archive/refs/tags/v${VCF2MAF_VERSION}.zip" && \
+    curl -L "https://github.com/mskcc/vcf2maf/archive/refs/tags/v${VCF2MAF_VERSION}.zip" -o vcf2maf.zip && \
+    unzip vcf2maf.zip && \
+    mv "vcf2maf-${VCF2MAF_VERSION}" vcf2maf && \
+    mkdir -p /opt/data && \
+    cp vcf2maf/*.pl /opt && \
+    sed -i '/ --af_esp/d' /opt/vcf2maf.pl && \
+    cp -r vcf2maf/data /opt/data && \
+    rm -rf vcf2maf
+
+# Download Cromwell + WOMtool
+ENV CROMWELL_VERSION=86
+WORKDIR /
+RUN curl -L \
+    https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/cromwell-${CROMWELL_VERSION}.jar \
+    -o cromwell.jar && \
+    curl -L \
+    https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/womtool-${CROMWELL_VERSION}.jar \
+    -o womtool.jar
+
+
+# Clone (but don't install yet) Ensembl-VEP
+ENV VEP_ENSEMBL_GIT_VERSION=111.0
+RUN git clone --depth 1 -b "release/${VEP_ENSEMBL_GIT_VERSION}" https://github.com/Ensembl/ensembl-vep.git && \
+    chmod u+x ensembl-vep/*.pl
+
+# Clone ensembl-variation git repository
+WORKDIR /ensembl-vep/
+RUN git clone --depth 1 https://github.com/Ensembl/ensembl-variation.git && \
+    mkdir var_c_code && \
+    cp ensembl-variation/C_code/*.c ensembl-variation/C_code/Makefile var_c_code/
+RUN git clone --depth 1 https://github.com/bioperl/bioperl-ext.git
+RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-xs.zip && \
+    unzip -q ensembl-xs.zip && \
+    mv ensembl-xs-2.3.2 ensembl-xs && \
+    rm -rf ensembl-xs.zip
+
+WORKDIR /
+
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01 AS base-deps
 
 LABEL org.opencontainers.image.description="Local development image for Bento WES."
 LABEL devcontainer.metadata='[{ \
@@ -13,25 +64,46 @@ LABEL devcontainer.metadata='[{ \
 
 SHELL ["/bin/bash", "-c"]
 
+WORKDIR /
+
 # Install system packages for HTSLib + SAMtools + curl and jq for workflows
 # OpenJDK is for running WOMtool/Cromwell
+
+RUN apt-get update -y && \
+    apt-get install -y \
+        samtools \
+        tabix \
+        bcftools \
+        curl \
+        jq \
+        openjdk-17-jre \
+    && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install system packages for VEP
+# Perl/libdbi-perl/lib*-dev/cpanminus/unzip are for cBioPortal scripts / caches / utilities
+RUN apt-get update -y && \
+    apt-get install -y \
+        curl \
+        perl \
+        libdbd-mysql-perl \
+        libdbi-perl \
+        libjson-perl \
+        libwww-perl \
+        libperl-dev \
+        cpanminus \
+        unzip \
+        libbz2-dev \
+        liblzma-dev \
+        zlib1g-dev \
+    && \
+    rm -rf /var/lib/apt/lists/*
+
 # Then, install dependencies for running the Python server + Python workflow dependencies
 COPY container.requirements.txt .
-RUN apt-get update -y && \
-    apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \
-    rm -rf /var/lib/apt/lists/* && \
-    pip install --no-cache-dir -r /container.requirements.txt && \
+RUN pip install --no-cache-dir -r /container.requirements.txt && \
     rm /container.requirements.txt
 
-WORKDIR /
-ENV CROMWELL_VERSION=86
-RUN curl -L \
-    https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/cromwell-${CROMWELL_VERSION}.jar \
-    -o cromwell.jar && \
-    curl -L \
-    https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/womtool-${CROMWELL_VERSION}.jar \
-    -o womtool.jar
-
 FROM base-deps AS install
 
 # Backwards-compatible with old BentoV2 container layout
@@ -54,5 +126,18 @@ COPY run.dev.bash .
 # Tell the service that we're running a local development container
 ENV BENTO_CONTAINER_LOCAL=true
 
+# Copy from other stages last, since it means the stages can be built in parallel
+
+# - Copy VCF2MAF
+COPY --from=downloaded-deps /opt /opt
+
+# - Copy Cromwell + WOMtool
+COPY --from=downloaded-deps /cromwell.jar /cromwell.jar
+COPY --from=downloaded-deps /womtool.jar /womtool.jar
+
+# - Copy Ensembl-VEP
+COPY --from=ensemblorg/ensembl-vep:release_111.0 /usr/share/perl/5.34.0/CPAN /opt/vep
+COPY --from=ensemblorg/ensembl-vep:release_111.0 /opt/vep /opt/vep
+
 ENTRYPOINT [ "bash", "./entrypoint.bash" ]
 CMD [ "bash", "./run.dev.bash" ]