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Dockerfile
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FROM ensemblorg/ensembl-vep:release_110.1 as build
USER root
RUN apt update && \
apt install -y git autoconf libcurl4-openssl-dev && \
git clone --recurse-submodules https://github.com/samtools/htslib.git && \
git clone https://github.com/mawumag/bcftools.git && \
cd bcftools && \
autoheader && autoconf && ./configure && \
make
FROM ensemblorg/ensembl-vep:release_110.1 as anno-vep
COPY --from=build \
/opt/vep/.vep/bcftools/bcftools \
/usr/local/bin/
COPY --from=build \
/opt/vep/.vep/bcftools/misc/color-chrs.pl \
/opt/vep/.vep/bcftools/misc/gff2gff.py \
/opt/vep/.vep/bcftools/misc/guess-ploidy.py \
/opt/vep/.vep/bcftools/misc/plot-vcfstats \
/opt/vep/.vep/bcftools/misc/plot-roh.py \
/opt/vep/.vep/bcftools/misc/run-roh.pl \
/opt/vep/.vep/bcftools/misc/vcfutils.pl \
/usr/local/bin/
COPY --from=build \
/opt/vep/.vep/bcftools/doc/bcftools.1 \
/usr/local/share/man/man1/
COPY --from=build \
/opt/vep/.vep/bcftools/plugins/*.so \
/usr/local/libexec/bcftools/
USER root
RUN apt update && \
apt install -y python3 python3-pip zip && \
pip3 install pandas xlsxwriter genmod
FROM anno-vep as anno-vep-db
RUN INSTALL.pl -a cfp --PLUGINS all -s homo_sapiens -y GRCh38