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Dockerfile
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FROM ensemblorg/ensembl-vep:release_105.0
LABEL maintainer="John Garza <[email protected]>"
LABEL description="Vep helper image"
USER root
RUN apt-get update -y && apt-get install -y \
libfile-copy-recursive-perl \
libipc-run-perl \
wget
#necessary because some legacy cwl files still refer to vep (the current name) as variant_effect_predictor.pl
WORKDIR /
RUN ln -s /opt/vep/src/ensembl-vep/vep /usr/bin/variant_effect_predictor.pl
WORKDIR /opt/vep/src/ensembl-vep
RUN perl INSTALL.pl --NO_UPDATE
RUN mkdir -p /opt/lib/perl/VEP/Plugins
WORKDIR /opt/lib/perl/VEP/Plugins
RUN wget https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/Downstream.pm \
https://raw.githubusercontent.com/griffithlab/pVACtools/master/pvactools/tools/pvacseq/VEP_plugins/Wildtype.pm \
https://raw.githubusercontent.com/griffithlab/pVACtools/master/pvactools/tools/pvacseq/VEP_plugins/Frameshift.pm \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/CADD.pm \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/REVEL.pm \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/ExACpLI.pm \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/ExACpLI_values.txt \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/LoFtool.pm \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/LoFtool_scores.txt \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/SpliceRegion.pm \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/dbNSFP.pm \
https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/105/dbNSFP_replacement_logic
COPY vcf_check.pl /usr/bin/vcf_check.pl
USER vep