update install micromamba shell script
This commit is contained in:
@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
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COPY install.sh /tmp
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RUN <<EOT
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#!/bin/bash
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# 更新软件源
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@@ -95,7 +96,9 @@ useradd -m -s /bin/bash ${CREATE_USER}
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echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
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echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
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# 安装micromamba
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echo "1" | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
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echo "1" | bash /tmp/install.sh
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mkdir -p /home/${CREATE_USER}/micromamba
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chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
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# 安装 Jupyter 和相关软件
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npm install -g configurable-http-proxy
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python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
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@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
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COPY install.sh /tmp
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RUN <<EOT
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#!/bin/bash
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# 更新软件源
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@@ -95,10 +96,12 @@ useradd -m -s /bin/bash ${CREATE_USER}
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echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
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echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
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# 安装micromamba
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echo 1 | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
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echo "1" | bash /tmp/install.sh
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mkdir -p /home/${CREATE_USER}/micromamba
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chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
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# 安装 Jupyter 和相关软件
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npm install -g configurable-http-proxy
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python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
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python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
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EOT
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RUN <<EOT
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@@ -124,14 +127,6 @@ EOT
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# Switch back to jovyan to avoid accidental container runs as root
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USER ${NB_UID}
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ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
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RUN <<EOT
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#!/bin/bash
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sudo apt update
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sudo apt install -y texlive-full
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micromamba create -n plot -c conda-forge scienceplots autopep8 python=3 ipykernel pandas numpy matplotlib scipy seaborn orange3 -y
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micromamba run -n plot python -m pip install bamboolib
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micromamba run -n plot python -m ipykernel install --user --name="sciplot" --display-name="SCIPlot Environment"
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EOT
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# install mojo
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ENV PATH="/home/${CREATE_USER}/.local/bin:$PATH"
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@@ -152,15 +147,6 @@ modular auth $AUTH_KEY
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modular install mojo
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EOT
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RUN <<EOT
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#!/bin/bash
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micromamba create -n mixtral_env -c conda-forge ipykernel -y
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git clone https://github.com/Lightning-AI/lit-gpt.git
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cd lit-gpt
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micromamba run -n mixtral_env python -m pip install -r requirements.txt
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micromamba run -n mixtral_env python -m ipykernel install --user --name="mixtral" --display-name="mixtral Environment"
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EOT
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# Install Rust
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ENV PATH="/home/${CREATE_USER}/.cargo/bin:$PATH"
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RUN <<EOT
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@@ -171,11 +157,5 @@ cargo install evcxr_jupyter
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evcxr_jupyter --install
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EOT
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RUN <<EOT
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#!/bin/bash
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micromamba create -n mdgnn -c pytorch -c conda-forge python=3.9 pytorch=1.10.2 torchvision torchaudio cudatoolkit=11.3 pandas matplotlib seaborn scipy numpy=1.24.4 mdanalysis biopandas pymol-open-source ipykernel ipywidgets jupyter einops python-calamine scikit-learn -y
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micromamba run -n mdgnn python -m ipykernel install --user --name="mdgnn" --display-name="mdgnn Environment"
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EOT
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WORKDIR "${HOME}"
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@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
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COPY install.sh /tmp
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RUN <<EOT
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#!/bin/bash
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# 更新软件源
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@@ -95,82 +96,17 @@ useradd -m -s /bin/bash ${CREATE_USER}
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echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
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echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
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# 安装micromamba
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echo "1" | bash <(curl -s https://raw.githubusercontent.com/hotwa/MicroMamba_Installer/main/install.sh)
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echo "1" | bash /tmp/install.sh
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mkdir -p /home/${CREATE_USER}/micromamba
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chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
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# 安装 Jupyter 和相关软件
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npm install -g configurable-http-proxy
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python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
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EOT
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RUN <<EOT
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#!/bin/bash
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# install rserver
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apt update
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apt update -qq
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apt install -y --no-install-recommends software-properties-common dirmngr
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wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
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echo | add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
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apt-get update
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apt install -y --no-install-recommends r-base
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wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/rstudio-server-2023.06.1-524-amd64.deb" -O /tmp/rstudio-server.deb
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chmod +x /tmp/rstudio-server.deb
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gdebi -n /tmp/rstudio-server.deb
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rm -rf /tmp/rstudio-server.deb
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chown -R ${CREATE_USER}:users /home/${CREATE_USER}
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# 清理和减小镜像大小
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/man/?? /usr/share/man/??_*
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python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
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EOT
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# Switch back to jovyan to avoid accidental container runs as root
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USER ${NB_UID}
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ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
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RUN <<EOT
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#!/bin/bash
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sudo apt update
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sudo apt install -y texlive-full
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micromamba create -n plot -c conda-forge scienceplots autopep8 python=3 ipykernel pandas numpy matplotlib scipy seaborn orange3 -y
|
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micromamba run -n plot python -m pip install bamboolib
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micromamba run -n plot python -m ipykernel install --user --name="sciplot" --display-name="SCIPlot Environment"
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EOT
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# install mojo
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ENV PATH="/home/${CREATE_USER}/.local/bin:$PATH"
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# A random default token
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ARG AUTH_KEY=5ca1ab1e
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ENV AUTH_KEY=$AUTH_KEY
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RUN curl https://get.modular.com | sh - && \
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modular auth $AUTH_KEY
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RUN
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ARG MODULAR_HOME="/home/${CREATE_USER}/.modular"
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ENV MODULAR_HOME=$MODULAR_HOME
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ENV PATH="$PATH:$MODULAR_HOME/pkg/packages.modular.com_mojo/bin"
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RUN <<EOT
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#!/bin/bash
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curl https://get.modular.com | sh - && \
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modular auth $AUTH_KEY
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modular install mojo
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EOT
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RUN <<EOT
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#!/bin/bash
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micromamba create -n mixtral_env -c conda-forge ipykernel -y
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git clone https://github.com/Lightning-AI/lit-gpt.git
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cd lit-gpt
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micromamba run -n mixtral_env python -m pip install -r requirements.txt
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micromamba run -n mixtral_env python -m ipykernel install --user --name="mixtral" --display-name="mixtral Environment"
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EOT
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# Install Rust
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RUN <<EOT
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#!/bin/bash
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curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
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source $HOME/.cargo/env
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cargo install evcxr_jupyter
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evcxr_jupyter --install
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EOT
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RUN <<EOT
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#!/bin/bash
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micromamba create -n mdgnn -c pytorch -c conda-forge python=3.9 pytorch=1.10.2 torchvision torchaudio cudatoolkit=11.3 pandas matplotlib seaborn scipy numpy=1.24.4 mdanalysis biopandas pymol-open-source ipykernel ipywidgets jupyter -y
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@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
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COPY install.sh /tmp
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RUN <<EOT
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#!/bin/bash
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# 更新软件源
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@@ -95,7 +96,9 @@ useradd -m -s /bin/bash ${CREATE_USER}
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echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
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echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
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# 安装micromamba
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echo "1" | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
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echo "1" | bash /tmp/install.sh
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mkdir -p /home/${CREATE_USER}/micromamba
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chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
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# 安装 Jupyter 和相关软件
|
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npm install -g configurable-http-proxy
|
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python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
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229
spawnerdockerfile/install.sh
Executable file
229
spawnerdockerfile/install.sh
Executable file
@@ -0,0 +1,229 @@
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#!/bin/bash
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# 安装所需依赖
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install_dependencies() {
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# 检查并安装 jq, curl, tar, bzip2
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for dep in jq curl tar bzip2; do
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if ! command -v $dep >/dev/null 2>&1; then
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sudo apt-get update && sudo apt-get install -y $dep
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fi
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done
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}
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# 在脚本开始时调用依赖安装函数
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install_dependencies
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# 默认的MAMBA_ROOT_PREFIX路径
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DEFAULT_MAMBA_ROOT_PREFIX="/usr/local/bin"
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# 显示用法信息
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usage() {
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echo "用法: sudo $0 [--silent-install [custom_root_prefix]] [--silent-uninstall] [--silent-update]"
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echo " --silent-install 静默模式安装，不进行任何交互"
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echo " custom_root_prefix (可选) 在静默模式下设置 MAMBA_ROOT_PREFIX 的路径"
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echo " --silent-uninstall 静默模式卸载，不进行任何交互"
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echo " --silent-update 静默模式更新，不进行任何交互"
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exit 1
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}
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# 安装micromamba
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install_micromamba() {
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local mamba_prefix="$1"
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# 自动检测操作系统和处理器架构
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OS="$(uname)"
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ARCH="$(uname -m)"
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# 根据操作系统和架构设置下载链接
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case "$OS" in
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"Linux")
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case "$ARCH" in
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"x86_64") URL="https://micro.mamba.pm/api/micromamba/linux-64/latest" ;;
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"aarch64") URL="https://micro.mamba.pm/api/micromamba/linux-aarch64/latest" ;;
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"ppc64le") URL="https://micro.mamba.pm/api/micromamba/linux-ppc64le/latest" ;;
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*) echo "不支持的架构: $ARCH"; exit 1 ;;
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esac
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;;
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"Darwin")
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case "$ARCH" in
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"x86_64") URL="https://micro.mamba.pm/api/micromamba/osx-64/latest" ;;
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"arm64") URL="https://micro.mamba.pm/api/micromamba/osx-arm64/latest" ;;
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*) echo "不支持的架构: $ARCH"; exit 1 ;;
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esac
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;;
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*)
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echo "不支持的操作系统: $OS"; exit 1 ;;
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esac
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# 下载并解压 micromamba 到指定的路径
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echo "正在下载 micromamba..."
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if curl -Ls "$URL" | tar -xvj -C "$mamba_prefix"; then
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echo "micromamba 下载并解压完成。"
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ls -l /usr/local/bin/bin/micromamba
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echo "micromamba 赋予执行权限"
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chmod +x /usr/local/bin/bin/micromamba
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echo "micromamba 安装完成"
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echo "MAMBA_ROOT_PREFIX 路径：$mamba_prefix"
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# 初始化 shell 环境
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echo "正在为root初始化 micromamba shell 环境..."
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"$mamba_prefix/bin/micromamba" shell init -s bash -p "~/micromamba"
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ln -s /usr/local/bin/bin/micromamba /usr/local/bin/micromamba
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else
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echo "micromamba 下载失败"
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fi
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}
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# 清理 .bashrc 文件
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cleanup_bashrc() {
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local mamba_bin_path="$1"
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# 删除 .bashrc 中相关的行
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sed -i '/MICROMAMBA_BIN_PATH/d' ~/.bashrc
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sed -i '/MAMBA_ROOT_PREFIX/d' ~/.bashrc
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sed -i '/alias mba=/d' ~/.bashrc
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}
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# 删除micromamba
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uninstall_micromamba() {
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echo "正在卸载 micromamba..."
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rm -rf /usr/local/bin/micromamba /usr/local/bin/bin /usr/local/bin/info /usr/local/bin/etc
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# 清理 .bashrc 文件
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cleanup_bashrc "$mamba_prefix"
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echo "micromamba 已卸载。"
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}
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||||
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# 获取当前 micromamba 版本
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get_current_version() {
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local mamba_path="$1/micromamba"
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if [ -f "$mamba_path" ]; then
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local current_version
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||||
current_version=$("$mamba_path" --version | grep -o 'version [^ ]*' | cut -d ' ' -f2 | cut -d '-' -f1)
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||||
echo "$current_version"
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||||
else
|
||||
echo "未安装"
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||||
fi
|
||||
}
|
||||
|
||||
# 获取最新的 micromamba 版本
|
||||
get_latest_version() {
|
||||
local latest_version
|
||||
latest_version=$(curl -s https://api.github.com/repos/mamba-org/micromamba-releases/releases/latest | jq -r '.tag_name' | cut -d '-' -f1)
|
||||
echo "$latest_version"
|
||||
}
|
||||
|
||||
# 检查是否有更新并提示用户
|
||||
check_for_updates() {
|
||||
local current_version latest_version
|
||||
current_version=$(get_current_version "$1")
|
||||
latest_version=$(get_latest_version)
|
||||
|
||||
if [ "$latest_version" != "$current_version" ]; then
|
||||
echo "有可用的更新：当前版本 $current_version, 最新版本 $latest_version"
|
||||
read -p "是否更新到最新版本? (y/N): " confirm
|
||||
if [[ "$confirm" =~ ^[Yy]$ ]]; then
|
||||
update_micromamba "$1"
|
||||
else
|
||||
echo "更新已取消"
|
||||
fi
|
||||
else
|
||||
echo "当前已是最新版本 ($current_version)"
|
||||
fi
|
||||
}
|
||||
|
||||
# 更新micromamba
|
||||
update_micromamba() {
|
||||
local mamba_prefix="$1"
|
||||
local current_version latest_version
|
||||
current_version=$(get_current_version "$mamba_prefix")
|
||||
latest_version=$(get_latest_version)
|
||||
|
||||
if [ "$latest_version" != "$current_version" ]; then
|
||||
echo "有可用的更新：当前版本 $current_version, 最新版本 $latest_version"
|
||||
read -p "是否更新到最新版本? (y/N): " confirm
|
||||
if [[ "$confirm" =~ ^[Yy]$ ]]; then
|
||||
echo "正在卸载旧版本 micromamba..."
|
||||
uninstall_micromamba "$mamba_prefix"
|
||||
echo "正在安装最新版本 micromamba..."
|
||||
install_micromamba "$mamba_prefix"
|
||||
else
|
||||
echo "更新已取消"
|
||||
fi
|
||||
else
|
||||
echo "当前已是最新版本 ($current_version)"
|
||||
fi
|
||||
}
|
||||
|
||||
|
||||
# 交互式安装、卸载和更新菜单
|
||||
interactive_menu() {
|
||||
local current_version latest_version
|
||||
current_version=$(get_current_version "$DEFAULT_MAMBA_ROOT_PREFIX")
|
||||
latest_version=$(get_latest_version)
|
||||
|
||||
# 检测并显示当前和最新版本
|
||||
echo "当前 micromamba 版本: $current_version"
|
||||
echo "最新 micromamba 版本: $latest_version"
|
||||
if [ "$latest_version" != "$current_version" ]; then
|
||||
echo "有可用的更新。"
|
||||
fi
|
||||
|
||||
echo "选择操作："
|
||||
echo "1) 安装 micromamba"
|
||||
echo "2) 删除 micromamba"
|
||||
echo "3) 更新 micromamba"
|
||||
echo "q) 退出"
|
||||
read -p "请输入选项（1、2、3或q）: " main_choice
|
||||
|
||||
case "$main_choice" in
|
||||
1)
|
||||
echo "MAMBA_ROOT_PREFIX 的路径: $DEFAULT_MAMBA_ROOT_PREFIX: "
|
||||
install_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
|
||||
;;
|
||||
2)
|
||||
uninstall_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
|
||||
;;
|
||||
3)
|
||||
update_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
|
||||
;;
|
||||
q)
|
||||
echo "退出。"
|
||||
exit 0
|
||||
;;
|
||||
*)
|
||||
echo "无效的选项。退出。"
|
||||
exit 1
|
||||
;;
|
||||
esac
|
||||
}
|
||||
|
||||
# 静默卸载
|
||||
silent_uninstall() {
|
||||
# 在卸载之前保留虚拟环境目录
|
||||
local envs_dir="$DEFAULT_MAMBA_ROOT_PREFIX/envs"
|
||||
mkdir -p "$envs_dir"
|
||||
mv "$DEFAULT_MAMBA_ROOT_PREFIX/envs" "$(mktemp -d)"
|
||||
uninstall_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
|
||||
mv "$(mktemp -d)/envs" "$envs_dir"
|
||||
}
|
||||
|
||||
# 静默更新
|
||||
silent_update() {
|
||||
update_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
|
||||
}
|
||||
|
||||
# 解析命令行参数
|
||||
if [ "$1" = "--silent-install" ]; then
|
||||
silent_install "$2"
|
||||
elif [ "$1" = "--silent-uninstall" ]; then
|
||||
silent_uninstall
|
||||
elif [ "$1" = "--silent-update" ]; then
|
||||
silent_update
|
||||
elif [ "$1" = "--help" ]; then
|
||||
usage
|
||||
else
|
||||
interactive_menu
|
||||
fi
|
||||
Reference in New Issue
Block a user