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fix: use mambaforge for snakemake container image (#1595)
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johanneskoester committed Apr 22, 2022
1 parent a107fe4 commit b7e6906926cae5fef6987adcf7b0294266d5faec
Showing 1 changed file with 4 additions and 5 deletions.
@@ -6,11 +6,10 @@ ENV PATH /opt/conda/bin:${PATH}
ENV LANG C.UTF-8
ENV SHELL /bin/bash
RUN install_packages wget curl bzip2 ca-certificates gnupg2 squashfs-tools git
RUN /bin/bash -c "curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh && \
bash miniconda.sh -b -p /opt/conda && \
rm miniconda.sh"
RUN /bin/bash -c "conda install -y -c conda-forge mamba && \
mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake snakemake-minimal --only-deps && \
RUN /bin/bash -c "curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh > mambaforge.sh && \
bash mambaforge.sh -b -p /opt/conda && \
rm mambaforge.sh"
RUN /bin/bash -c "mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake snakemake-minimal --only-deps && \
source activate snakemake && \
mamba install -q -y -c conda-forge singularity && \
conda clean --all -y && \

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