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Dockerfile
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FROM rocker/geospatial:3.5.1
ARG arg_minicondaversion=4.5.12
ARG arg_gitlfsversion=2.6.0
ENV minicondaversion=${arg_minicondaversion}
ENV gitlfsversion=${arg_gitlfsversion}
ENV condaprefix=/opt/conda
ENV CONDA_ENVS_PATH=${condaprefix}/envs
RUN apt-get update && apt-get install time
# install git LFS
RUN wget --quiet https://github.com/git-lfs/git-lfs/releases/download/v${gitlfsversion}/git-lfs-linux-amd64-v${gitlfsversion}.tar.gz && \
tar xvf git-lfs-linux-amd64-v${gitlfsversion}.tar.gz \
-C /usr/local/bin/ \
git-lfs && \
rm git-lfs-linux-amd64-v${gitlfsversion}.tar.gz
# install miniconda
RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${minicondaversion}-Linux-x86_64.sh && \
/bin/bash Miniconda3-${minicondaversion}-Linux-x86_64.sh -f -b -p ${condaprefix} && \
rm Miniconda3-${minicondaversion}-Linux-x86_64.sh
ENV PATH=${condaprefix}/bin:$PATH
RUN conda install -c bioconda -y biopython=1.72 \
bowtie2=2.3.4.3 \
gatk4=4.1.0.0 \
jupyter=1.0.0 \
matplotlib=3.0.2 \
picard=2.18.26 \
pandas=0.24.1 \
samtools=1.9 \
scipy=1.2.0 \
sra-tools=2.9.1_1 \
&& \
conda clean -tipsy