use mamba

Dockerfile

@@ -102,6 +102,8 @@ RUN yum install -y -q \
     && bash "$conda_installer" -b -p /opt/miniconda-latest \
     && rm -f "$conda_installer" \
     && conda update -yq -nbase conda \
+    && conda install -yq -nbase conda-libmamba-solver \
+    && conda config --set solver libmamba \
     # Prefer packages in conda-forge
     && conda config --system --prepend channels conda-forge \
     # Packages in lower-priority channels not considered if a package with the same
@@ -218,7 +220,7 @@ RUN printf '{ \
     { \
       "name": "run", \
       "kwds": { \
-        "command": "yum install -y -q \\\\\\n    bzip2 \\\\\\n    curl\\nyum clean all\\nrm -rf /var/cache/yum/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y  --name base \\\\\\n    \\"python=3.10\\" \\\\\\n    \\"pip=23.2.1\\"\\nbash -c \\"source activate base\\n  python -m pip install --no-cache-dir  \\\\\\n      \\"traits==6.3.0\\" \\\\\\n      \\"jupyterlab-4.0.6\\" \\\\\\n      \\"graphviz-0.20.1\\" \\\\\\n      \\"nipype==1.8.6\\" \\\\\\n      \\"scikit-image==0.21.0\\" \\\\\\n      \\"matplotlib==3.8.0\\" \\\\\\n      \\"nilearn==0.10.1\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
+        "command": "yum install -y -q \\\\\\n    bzip2 \\\\\\n    curl\\nyum clean all\\nrm -rf /var/cache/yum/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\nconda install -yq -nbase conda-libmamba-solver\\nconda config --set solver libmamba\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y  --name base \\\\\\n    \\"python=3.10\\" \\\\\\n    \\"pip=23.2.1\\"\\nbash -c \\"source activate base\\n  python -m pip install --no-cache-dir  \\\\\\n      \\"traits==6.3.0\\" \\\\\\n      \\"jupyterlab-4.0.6\\" \\\\\\n      \\"graphviz-0.20.1\\" \\\\\\n      \\"nipype==1.8.6\\" \\\\\\n      \\"scikit-image==0.21.0\\" \\\\\\n      \\"matplotlib==3.8.0\\" \\\\\\n      \\"nilearn==0.10.1\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
       } \
     }, \
     { \

makefile

@@ -2,6 +2,20 @@
 
 Dockerfile:
 	docker run --rm repronim/neurodocker:0.9.5 generate docker \
+			--base-image centos:7 --pkg-manager yum \
+			--yes \
+			--install git \
+			--ants method=binaries version=2.4.3 \
+			--fsl version=6.0.6.4 \
+			--spm12 version=r7771 method=binaries \
+			--miniconda method=binaries \
+						version=latest 
+						conda_install="python=3.10 pip=23.2.1" \
+						pip_install="traits==6.3.0 jupyterlab-4.0.6 graphviz-0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \
+			--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile
+
+Dockerfile_mamba:
+	neurodocker generate docker \
 			--base-image centos:7 --pkg-manager yum \
 			--yes \
 			--install git \
@@ -10,6 +24,7 @@ Dockerfile:
 			--spm12 version=r7771 method=binaries \
 			--miniconda method=binaries \
 						version=latest \
+						mamba=true \
 						conda_install="python=3.10 pip=23.2.1" \
 						pip_install="traits==6.3.0 jupyterlab-4.0.6 graphviz-0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \
 			--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile