diff --git a/Dockerfile b/Dockerfile index 4cf7cae..5750759 100644 --- a/Dockerfile +++ b/Dockerfile @@ -30,7 +30,6 @@ RUN curl -L \ # Clone (but don't install yet) Ensembl-VEP -ENV VEP_ENSEMBL_VERSION=111 ENV VEP_ENSEMBL_GIT_VERSION=111.0 RUN git clone --depth 1 -b "release/${VEP_ENSEMBL_GIT_VERSION}" https://github.com/Ensembl/ensembl-vep.git && \ chmod u+x ensembl-vep/*.pl @@ -46,14 +45,6 @@ RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-x mv ensembl-xs-2.3.2 ensembl-xs && \ rm -rf ensembl-xs.zip -WORKDIR /vep-cache - -# Download GRCh38 VEP cache -ENV VEP_CACHE_BASE_URL="https://ftp.ensembl.org/pub/release-${VEP_ENSEMBL_VERSION}/variation/indexed_vep_cache" -ENV VEP_CACHE_ARCHIVE="homo_sapiens_vep_${VEP_ENSEMBL_VERSION}_GRCh38.tar.gz" -RUN curl -O "${VEP_CACHE_BASE_URL}/${VEP_CACHE_ARCHIVE}" && \ - tar xzvf "${VEP_CACHE_ARCHIVE}" - WORKDIR / FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01 AS base-deps @@ -138,8 +129,6 @@ 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 -COPY --from=downloaded-deps /vep-cache /vep-cache -ENV VEP_CACHE_DIR=/vep-cache ENTRYPOINT [ "bash", "./entrypoint.bash" ] CMD [ "bash", "./run.bash" ] diff --git a/dev.Dockerfile b/dev.Dockerfile index ab8b8ea..b1356f9 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -30,7 +30,6 @@ RUN curl -L \ # Clone (but don't install yet) Ensembl-VEP -ENV VEP_ENSEMBL_VERSION=111 ENV VEP_ENSEMBL_GIT_VERSION=111.0 RUN git clone --depth 1 -b "release/${VEP_ENSEMBL_GIT_VERSION}" https://github.com/Ensembl/ensembl-vep.git && \ chmod u+x ensembl-vep/*.pl @@ -46,14 +45,6 @@ RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-x mv ensembl-xs-2.3.2 ensembl-xs && \ rm -rf ensembl-xs.zip -WORKDIR /vep-cache - -# Download GRCh38 VEP cache -ENV VEP_CACHE_BASE_URL="https://ftp.ensembl.org/pub/release-${VEP_ENSEMBL_VERSION}/variation/indexed_vep_cache" -ENV VEP_CACHE_ARCHIVE="homo_sapiens_vep_${VEP_ENSEMBL_VERSION}_GRCh38.tar.gz" -RUN curl -O "${VEP_CACHE_BASE_URL}/${VEP_CACHE_ARCHIVE}" && \ - tar xzvf "${VEP_CACHE_ARCHIVE}" - WORKDIR / FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01 AS base-deps @@ -145,8 +136,6 @@ 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 -COPY --from=downloaded-deps /vep-cache /vep-cache -ENV VEP_CACHE_DIR=/vep-cache ENTRYPOINT [ "bash", "./entrypoint.bash" ] CMD [ "bash", "./run.dev.bash" ]