add remove

spawnerdockerfile/Dockerfile.base-notebook

@@ -88,20 +88,17 @@ ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
 echo 'Asia/Shanghai' > /etc/timezone
 dpkg-reconfigure -f noninteractive tzdata
 # 安装所需的软件包
-apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git texlive-full
+apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git
 # 创建新用户
 useradd -m -s /bin/bash ${CREATE_USER}
 echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
 echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
-# 安装micromamba
-echo "1" | bash <(curl -s https://raw.githubusercontent.com/hotwa/MicroMamba_Installer/main/install.sh)
+# # 安装micromamba
+# echo "1" | bash <(curl -s https://raw.githubusercontent.com/hotwa/MicroMamba_Installer/main/install.sh)
 # 安装 Jupyter 和相关软件
 npm install -g configurable-http-proxy
-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
-EOT
-
-RUN <<EOT
-#!/bin/bash
+python3 -m pip install --default-timeout=10000 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 https://pypi.tuna.tsinghua.edu.cn/simple
 # install rserver
 apt update 
 apt update -qq
@@ -114,10 +111,6 @@ wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/rstudio-serv
 chmod +x /tmp/rstudio-server.deb 
 gdebi -n /tmp/rstudio-server.deb
 rm -rf /tmp/rstudio-server.deb
-EOT
-
-RUN <<EOT
-#!/bin/bash
 chown -R ${CREATE_USER}:users /home/${CREATE_USER}
 # 清理和减小镜像大小
 apt-get clean 
@@ -126,9 +119,24 @@ EOT
 
 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}
-ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
+ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/mamba
+
+# add pdb env
 RUN <<EOT
 #!/bin/bash
+mamba create -n pdbfixer_env -c conda-forge pdbfixer openmm pymol-open-source rdkit openbabel ipykernel -y
+mamba run -n pdbfixer_env python -m ipykernel install --user --name="pdbfixer" --display-name="PDBfixer Environment"
+mamba create -n scardock_env -c conda-forge -c bioconda -c pylyzeng vinautil ipykernel -y
+mamba run -n scardock_env python -m ipykernel install --user --name="scardock" --display-name="SCARdock Environment"
+mamba create -n fpocket_env -c conda-forge fpocket ipykernel -y
+mamba run -n fpocket_env python -m ipykernel install --user --name="fpocket" --display-name="fpocket Environment"
+EOT
+
+# SCIplot env
+RUN <<EOT
+#!/bin/bash
+sudo apt update
+sudo apt install -y texlive-full
 micromamba create -n plot -c conda-forge scienceplots autopep8 python=3 ipykernel pandas numpy matplotlib scipy seaborn orange3 -y
 micromamba run -n plot python -m pip install bamboolib
 micromamba run -n plot python -m ipykernel install --user --name="sciplot" --display-name="SCIPlot Environment"