Update dna_toolbox.dockerfile

uzh-dqbm-cmi · Feb 25, 2024 · 4a2be47 · 4a2be47
1 parent d5a2f91
commit 4a2be47
Showing 1 changed file with 18 additions and 14 deletions.
diff --git a/bioinformatics/dna_toolbox.dockerfile b/bioinformatics/dna_toolbox.dockerfile
@@ -12,35 +12,39 @@ 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
 
 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