mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-31 03:32:10 -05:00
41 lines
1.5 KiB
Text
41 lines
1.5 KiB
Text
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# 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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