shl198/vep_loftee repository overview

⁠VEP annotation based on GRCh38.

The version 97.4_ExACpLI includes vep97.4, for plugin ExACpLI, it has the raw file provided by VEP.

FROM ensemblorg/ensembl-vep:release_109.3

MAINTAINER ShangzhongLi [email protected]⁠

ENV PATH=/opt/miniconda/bin:$PATH ENV PATH=/opt/vep/src/ensembl-vep:$PATH ENV BCFTOOLS_VERSION=1.18 ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64

⁠install conda

SHELL ["/bin/bash", "-c"]

RUN apt update && apt install -y wget git gcc make openjdk-11-jre-headless

RUN cd /opt &&
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py39_23.1.0-1-Linux-x86_64.sh⁠ &&
chmod 755 Miniconda3-py39_23.1.0-1-Linux-x86_64.sh &&
./Miniconda3-py39_23.1.0-1-Linux-x86_64.sh -b -p /opt/miniconda &&
rm Miniconda3-py39_23.1.0-1-Linux-x86_64.sh &&
eval "$(/opt/miniconda/bin/conda shell.bash hook)" &&
# download vep plugin git clone --branch release/110 https://github.com/Ensembl/VEP_plugins.git⁠ &&
mkdir .vep &&
mv VEP_plugins Plugins &&
mv Plugins .vep

RUN cd /opt &&
wget -O bcftools-${BCFTOOLS_VERSION}.tar.bz2 https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2⁠ &&
tar -xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 &&
rm bcftools-${BCFTOOLS_VERSION}.tar.bz2 &&
cd bcftools-${BCFTOOLS_VERSION} &&
./configure --prefix=/opt/bcftools-${BCFTOOLS_VERSION} &&
make &&
make install

RUN conda install -y -c bioconda vt &&
conda install -y -c bioconda nextflow=23.04.1

RUN ln -s /opt/vep/src/ensembl-vep/vep /usr/local/bin/vep &&
ln -s /opt/miniconda/bin/nextflow /usr/local/bin/nextflow &&
ln -s /opt/miniconda/bin/vt /usr/local/bin/vt

CMD ["/bin/bash"]