From b7e6906926cae5fef6987adcf7b0294266d5faec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 22 Apr 2022 14:31:38 +0200 Subject: [PATCH] fix: use mambaforge for snakemake container image (#1595) --- Dockerfile | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index ab4277a27..b7427a1c0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 && \