diff --git a/bioinformatics/dna_toolbox.dockerfile b/bioinformatics/dna_toolbox.dockerfile index cde4d65..692fc14 100644 --- a/bioinformatics/dna_toolbox.dockerfile +++ b/bioinformatics/dna_toolbox.dockerfile @@ -12,27 +12,31 @@ RUN apt-get install -y git RUN apt-get install -y curl ## 3.9: https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh -RUN curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o Miniconda3-latest-Linux-x86_64.sh -RUN chmod +x Miniconda3-latest-Linux-x86_64.sh -RUN ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3 +#RUN curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o Miniconda3-latest-Linux-x86_64.sh +#RUN chmod +x Miniconda3-latest-Linux-x86_64.sh +#RUN ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3 +## start with mamba +curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh" +chmod +x Mambaforge-Linux-x86_64.sh +./Mambaforge-Linux-x86_64.sh -p /opt/mambaforge -RUN export PATH=/opt/miniconda3/bin:$PATH +RUN export PATH=/opt/mambaforge/bin:$PATH # take too much time, avoid if not needed -RUN /opt/miniconda3/bin/conda update -n base -c defaults conda +RUN /opt/mambaforge/bin/conda update -n base -c defaults conda -RUN /opt/miniconda3/bin/conda config --add channels conda-forge -RUN /opt/miniconda3/bin/conda config --add channels bioconda -RUN /opt/miniconda3/bin/conda config --add channels anaconda -RUN /opt/miniconda3/bin/conda config --add channels r -RUN /opt/miniconda3/bin/conda update --all +#RUN /opt/miniconda3/bin/conda config --add channels conda-forge +#RUN /opt/miniconda3/bin/conda config --add channels bioconda +#RUN /opt/miniconda3/bin/conda config --add channels anaconda +#RUN /opt/miniconda3/bin/conda config --add channels r +RUN /opt/mambaforge/bin/mamba update --all COPY bioinformatics/dna_toolbox_requirements.txt / COPY bioinformatics/dna_toolbox_install_packages.R / -RUN /opt/miniconda3/bin/conda install --file /dna_toolbox_requirements.txt -RUN /opt/miniconda3/bin/conda install -c conda-forge mamba -RUN /opt/miniconda3/bin/mamba install snakemake -c conda-forge -c bioconda +RUN /opt/mambaforge/bin/mamba install --file /dna_toolbox_requirements.txt +#RUN /opt/miniconda3/bin/conda install -c conda-forge mamba +RUN /opt/mambaforge/bin/mamba install snakemake -c conda-forge -c bioconda # RUN /opt/miniconda3/bin/conda create -n LIQUORICE -c bioconda -c conda-forge liquorice ray RUN R -f /dna_toolbox_install_packages.R @@ -40,7 +44,7 @@ RUN apt-get autoremove -y RUN apt-get clean # check all is there -CMD conda list +CMD mamba list CMD python --version CMD pip --version CMD Rscript --version