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1b24005f07
* refactor: add bcl2fastq to cellranger dockerfile bcl2fastq required for the cellranger mkfastq module and was therefore added to the cellranger dockerfile. Further, cellranger was updated to the latest version, 6.1.2., with naming and containers across cellranger modules updated accordingly. * chore: add bcl2fastq zip to .gitignore * style: fix code linting error * test(cellranger): Add tiles to mkfastq * additional dockerfile for mkfastq * update readme and dockerfiles * update readme * fix: update container for mkfastq * docs: correct typos in readme * test: update md5sum following cellranger update * test: update md5sum following cellranger update * fix: new line for external args in mkfastq * test: update mkfastq tiles argument * test: comment out mkfastq tests until smaller test data found * test: stub-run mkfastq test until smaller test data found * test: fix incorrect file path for mkfastq Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
40 lines
1.5 KiB
Docker
40 lines
1.5 KiB
Docker
# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
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# Push to nfcore/cellrangermkfastq:<VER>
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FROM continuumio/miniconda3:4.8.2
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LABEL authors="Regina Reynolds, Gisela Gabernet <gisela.gabernet@gmail.com>" \
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description="Docker image containing bcl2fastq2 and Cell Ranger"
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# Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
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# Install procps and clean apt cache
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RUN apt-get update --allow-releaseinfo-change \
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&& apt-get install -y \
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cpio \
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procps \
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rpm2cpio \
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unzip \
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&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
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# Copy pre-downloaded bcl2fastq2 and cellranger file
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ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
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CELLRANGER_VER=6.1.2
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COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
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COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
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# Install bcl2fastq2
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RUN \
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cd /tmp && \
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unzip bcl2fastq2-$BCL2FASTQ2_VER.zip && \
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mv *.rpm bcl2fastq2-$BCL2FASTQ2_VER.rpm && \
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rpm2cpio ./bcl2fastq2-$BCL2FASTQ2_VER.rpm | cpio -idmv && \
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export PATH=/tmp/usr/local/bin/:$PATH && \
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ln -s /tmp/usr/local/bin/bcl2fastq /usr/bin/bcl2fastq && \
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rm -rf bcl2fastq2-$BCL2FASTQ2_VER.*
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# Install cellranger
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RUN \
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cd /opt && \
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tar -xzvf cellranger-$CELLRANGER_VER.tar.gz && \
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export PATH=/opt/cellranger-$CELLRANGER_VER:$PATH && \
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ln -s /opt/cellranger-$CELLRANGER_VER/cellranger /usr/bin/cellranger && \
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rm -rf /opt/cellranger-$CELLRANGER_VER.tar.gz
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