diff --git a/Dockerfile b/Dockerfile index 5750759..aefa456 100644 --- a/Dockerfile +++ b/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 '/ --af_esp/d' /opt/vcf2maf.pl && \ cp -r vcf2maf/data /opt/data && \ rm -rf vcf2maf diff --git a/dev.Dockerfile b/dev.Dockerfile index b1356f9..cf08193 100644 --- a/dev.Dockerfile +++ b/dev.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 '/ --af_esp/d' /opt/vcf2maf.pl && \ cp -r vcf2maf/data /opt/data && \ rm -rf vcf2maf