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Dockerfile
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#################################################################
# Dockerfile
#
# Software: VEP
# Software Version: 86
# Description: Variant Effect Predictor
# Website: http://uswest.ensembl.org/info/docs/tools/vep/index.html
# Base Image: ubuntu 14.04
# Run Cmd: docker run vep perl variant_effect_predictor.pl
#################################################################
FROM ubuntu:14.04
MAINTAINER Adam Struck <strucka@ohsu.edu>
ENV HOME /home
ENV VEP_PATH /home/vep
ENV PATH $VEP_PATH/htslib:$PATH
ENV PERL5LIB $VEP_PATH:/opt/lib/perl5:$PERL5LIB
# Install compiler and other dependencies
RUN apt-get update && \
apt-get install --yes \
build-essential \
libarchive-zip-perl \
libdbd-mysql-perl \
libjson-perl \
libwww-perl \
cpanminus \
zlib1g-dev \
git \
curl \
unzip && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
# set up variable for install
ENV ENSEMBL_TOOLS_VERSION=86
WORKDIR /opt/
# download vep
RUN curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/${ENSEMBL_TOOLS_VERSION}.tar.gz && \
tar -zxvf ${ENSEMBL_TOOLS_VERSION}.tar.gz && \
mkdir $VEP_PATH && \
mv ensembl-tools-release-${ENSEMBL_TOOLS_VERSION}/scripts/variant_effect_predictor/* $VEP_PATH && \
ln -s $VEP_PATH/variant_effect_predictor.pl /usr/local/bin/ && \
rm -rf *
# install perl dependencies
RUN cpanm --mirror http://cpan.metacpan.org -l /opt/ File::Copy::Recursive Module::Build && \
rm -rf ~/.cpanm
# install VEP and plugins
RUN cd $VEP_PATH && \
perl INSTALL.pl --AUTO ap --SPECIES homo_sapiens --ASSEMBLY GRCh37,GrCh38 --PLUGINS all -c /vep-cache
WORKDIR /tmp/
CMD ["variant_effect_predictor.pl"]