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Dockerfile.cromwell
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Dockerfile.cromwell
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FROM centos:7
LABEL maintainer="Jaeyoung Chun ([email protected])"
ARG CELLRANGER_VERSION
ARG VDJ_REFERENCE_VERSION
ARG DOWNLOAD_URL
ENV PATH /opt/cellranger-${CELLRANGER_VERSION}:$PATH
RUN yum group install -y "Development Tools" \
&& yum install -y which
# cell ranger binaries
RUN curl -o cellranger-${CELLRANGER_VERSION}.tar.gz ${DOWNLOAD_URL} \
&& tar xzf cellranger-${CELLRANGER_VERSION}.tar.gz \
&& rm -rf cellranger-${CELLRANGER_VERSION}.tar.gz \
&& mv cellranger-${CELLRANGER_VERSION} /opt/
# V(D)J GRCh38 Reference - 7.0.0 (May 17, 2022)
RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
&& tar xzf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
&& rm -rf refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
&& mv refdata-cellranger-vdj-GRCh38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
# V(D)J GRCm38 Reference - 7.0.0 (May 17, 2022)
RUN curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
&& tar xzf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
&& rm -rf refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION}.tar.gz \
&& mv refdata-cellranger-vdj-GRCm38-alts-ensembl-${VDJ_REFERENCE_VERSION} /opt/
WORKDIR /opt
# ENTRYPOINT [ "cellranger" ]