don't download VEP cache after all - too big

bento-platform · Apr 2, 2024 · f3265dd · f3265dd
1 parent ad7f2a1
commit f3265dd
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diff --git 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
@@ -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" ]