Created a Dockerfile for Sentieon tools

docker/sentieon/Dockerfile

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+FROM python:3.11-bookworm
+
+MAINTAINER Billy Rowell <[email protected]>
+
+ARG IMAGE_NAME
+ENV IMAGE_NAME "${IMAGE_NAME}"
+ARG IMAGE_TAG
+ENV IMAGE_TAG "${IMAGE_TAG}"
+
+RUN apt-get -qq update \
+		&& apt-get -qq install \
+		libjemalloc2 \
+		procps \
+		git \
+		build-essential \
+		zlib1g-dev \
+		liblzma-dev \
+		libbz2-dev \
+		libcurl4-openssl-dev \
+		tabix \
+		&& rm -rf /var/lib/apt/lists/*
+
+ARG SENTIEON_VERSION
+ENV SENTIEON_VERSION "${SENTIEON_VERSION}"
+RUN mkdir -p /opt/sentieon/ \
+	&& wget "https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-${SENTIEON_VERSION}.tar.gz" \
+	&& tar --no-same-owner -zxf sentieon-genomics-${SENTIEON_VERSION}.tar.gz --directory /opt/sentieon/ \
+	&& rm sentieon-genomics-${SENTIEON_VERSION}.tar.gz
+
+ARG SENTIEON_PACBIO_MODEL_VERSION
+ENV SENTIEON_PACBIO_MODEL_VERSION "${SENTIEON_PACBIO_MODEL_VERSION}"
+RUN mkdir -p /opt/sentieon/model \
+	&& wget "https://s3.amazonaws.com/sentieon-release/other/${SENTIEON_PACBIO_MODEL_VERSION}.bundle" \
+	&& mv "${SENTIEON_PACBIO_MODEL_VERSION}.bundle" /opt/sentieon/model/
+ENV MODEL_BUNDLE="/opt/sentieon/model/${SENTIEON_PACBIO_MODEL_VERSION}.bundle"
+
+ARG BCFTOOLS_VERSION
+RUN wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 \
+	&& tar --no-same-owner -jxvf bcftools-${BCFTOOLS_VERSION}.tar.bz2 --directory /opt \
+	&& rm bcftools-${BCFTOOLS_VERSION}.tar.bz2
+RUN cd /opt/bcftools-${BCFTOOLS_VERSION} \
+	&& make \
+	&& make install
+
+ARG BEDTOOLS_VERSION
+RUN wget https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/bedtools.static \
+	-O /usr/local/bin/bedtools \
+	&& chmod +x /usr/local/bin/bedtools
+
+ARG SENTIEON_SCRIPTS_GIT_HASH
+ENV SENTIEON_SCRIPTS_GIT_HASH "${SENTIEON_SCRIPTS_GIT_HASH}"
+WORKDIR /opt
+RUN git clone https://github.com/Sentieon/sentieon-scripts.git \
+	&& cd sentieon-scripts \
+	&& git checkout "${SENTIEON_SCRIPTS_GIT_HASH}" \
+	&& wget https://raw.githubusercontent.com/Sentieon/sentieon-cli/main/sentieon_cli/scripts/gvcf_combine.py \
+	&& mv gvcf_combine.py /opt/sentieon-scripts/dnascope_LongRead/ \
+	&& chmod +x /opt/sentieon-scripts/dnascope_LongRead/*.py \
+	&& chmod +x /opt/sentieon-scripts/dnascope_LongRead/*.sh
+ENV PATH ${PATH}:/opt/sentieon-scripts/dnascope_LongRead 
+
+ENV SENTIEON_INSTALL_DIR=/opt/sentieon/sentieon-genomics-$SENTIEON_VERSION
+ENV PATH $SENTIEON_INSTALL_DIR/bin/:$PATH
+ENV LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libjemalloc.so.2
+
+# A default jemalloc configuration that should work well for most use-cases, see http://jemalloc.net/jemalloc.3.html
+ENV MALLOC_CONF=metadata_thp:auto,background_thread:true,dirty_decay_ms:30000,muzzy_decay_ms:30000
+
+CMD ["/bin/bash"]

docker/sentieon/build.env

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+# Image revision
+IMAGE_BUILD=3
+
+# Tool versions
+SENTIEON_VERSION=202308.01
+SENTIEON_PACBIO_MODEL_VERSION=DNAscopePacBio2.0
+SENTIEON_SCRIPTS_GIT_HASH=8d33f29
+BCFTOOLS_VERSION=1.16
+BEDTOOLS_VERSION=2.31.0
+
+# Image info
+IMAGE_NAME=sentieon
+IMAGE_TAG=${SENTIEON_VERSION}_build${IMAGE_BUILD}