如何在rstudio服务器中使用mamba/conda包
如何在rstudio服务器中使用mamba/conda包
提问于 2022-05-11 21:46:50
我正在尝试写到dockerfile，以便从yaml安装conda环境，并在我的项目目录中运行rstudio服务器。我知道rstudio-服务器-conda，但希望能够使用单个dockerfile来创建映像。
Dockerfile
FROM rocker/rstudio-stable:devel
# Set working directory
WORKDIR ${HOME}
# Copy directory files to image
COPY . ${HOME}
# Copy repo into ${HOME}, make user own $HOME
USER root
# Install base utilities
RUN apt-get update && \
apt-get install -y wget && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
# Install miniconda
ENV CONDA_DIR /opt/conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
# Put conda in path so we can use conda activate
ENV PATH=$CONDA_DIR/bin:$PATH
# Install umamba
RUN conda install -y micromamba -c conda-forge
# Create a conda environment from the environment yml
COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
RUN micromamba create --yes --file /tmp/environment.yml && \
micromamba clean --all --yes
# Activate the conda environment
ARG MAMBA_DOCKERFILE_ACTIVATE=1
RUN chown -R ${NB_USER} . ${HOME}
USER ${NB_USER}
# Settings required for conda+rstudio
ENV RSTUDIO_WHICH_R=${CONDAENV}/bin/R
ENV RETICULATE_PYTHON=${CONDAENV}/bin/python
RUN echo rsession-which-r=${RSTUDIO_WHICH_R} > /etc/rstudio/rserver.conf && \
echo rsession-ld-library-path=${CONDAENV}/lib >> /etc/rstudio/rserver.conf && \
echo "R_LIBS_USER=${CONDAENV}/lib/R/library" > /home/rstudio/.Renviron
## Run an install.R script, if it exists.
#RUN if [ -f /R/install.R ]; then R --quiet -f /R/install.R; fienvironment.yml
channels:
- conda-forge
dependencies:
- r-devtools=2.4.3=r41hc72bb7e_0
- r-tidyverse=1.3.1=r41hc72bb7e_0dockerfile安装了rstudio和micromamba，但是当我尝试在环境yaml中导入的包中读取时，它们就找不到了。
# build image
docker build --tag umamba-rstudio -f Dockerfile .docker run --rm \
-e ENV_NAME=environment \
--mount type=bind,source="$(pwd)",destination=/home/rstudio \
-p 127.0.0.1:8787:8787 \
-e DISABLE_AUTH=true \
umamba-rstudio回答 1
Stack Overflow用户
发布于 2022-07-07 19:24:45
我将讨论两种方法：
- 对现有文件进行最小的更改
- 导致改进的Dockerfile和图像的更大更改
下面是更改最少的Dockerfile，其中3行更改后的行都附加了# DIFF: ...注释：
FROM rocker/rstudio-stable:devel
# Set working directory
WORKDIR ${HOME}
# Copy directory files to image
COPY . ${HOME}
# Copy repo into ${HOME}, make user own $HOME
USER root
# Install base utilities
RUN apt-get update && \
apt-get install -y wget && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
# Install miniconda
ENV CONDA_DIR /opt/conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda # DIFF: removed " && \" from end of line
# Put conda in path so we can use conda activate
ENV PATH=$CONDA_DIR/bin:$PATH
# Install umamba
RUN conda install -y micromamba -c conda-forge
# Create a conda environment from the environment yml
ENV MAMBA_ROOT_PREFIX="/opt/conda" # DIFF: added this line
COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
RUN micromamba install --prefix "$MAMBA_ROOT_PREFIX" --yes --file /tmp/environment.yml && \ # DIFF: added --prefix flag and argument
micromamba clean --all --yes
# Activate the conda environment
ARG MAMBA_DOCKERFILE_ACTIVATE=1
RUN chown -R ${NB_USER} . ${HOME}
USER ${NB_USER}
# Settings required for conda+rstudio
ENV RSTUDIO_WHICH_R=${CONDAENV}/bin/R
ENV RETICULATE_PYTHON=${CONDAENV}/bin/python
RUN echo rsession-which-r=${RSTUDIO_WHICH_R} > /etc/rstudio/rserver.conf && \
echo rsession-ld-library-path=${CONDAENV}/lib >> /etc/rstudio/rserver.conf && \
echo "R_LIBS_USER=${CONDAENV}/lib/R/library" > /home/rstudio/.Renviron
## Run an install.R script, if it exists.
#RUN if [ -f /R/install.R ]; then R --quiet -f /R/install.R; fi但我建议进行更多实质性的更改，以使Dockerfile更易于维护、减少构建时间和创建更小的映像。这个Dockerfile很大程度上是基于mamba-org/micromamba-docker on 在现有的Docker映像中添加micromamba的说明(公开:我维护mamba-org/micromamba-docker)。
# bring in the micromamba image so we can copy files from it
FROM mambaorg/micromamba:0.24.0 as micromamba
# This is the image we are going add micromaba to:
FROM rocker/rstudio-stable:devel
ARG MAMBA_USER=root
ARG MAMBA_USER_ID=0
ARG MAMBA_USER_GID=0
ENV MAMBA_USER=$MAMBA_USER
ENV MAMBA_ROOT_PREFIX="/opt/conda"
ENV MAMBA_EXE="/bin/micromamba"
COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
/usr/local/bin/_dockerfile_setup_root_prefix.sh && \
echo rsession-which-r=${RSTUDIO_WHICH_R} > /etc/rstudio/rserver.conf && \
echo rsession-ld-library-path=${CONDAENV}/lib >> /etc/rstudio/rserver.conf && \
echo "R_LIBS_USER=${CONDAENV}/lib/R/library" > /home/rstudio/.Renviron
SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
# populate the "base" conda environment:
USER $MAMBA_USER
COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
RUN micromamba install --yes --file /tmp/environment.yml && \
micromamba clean --all --yes
WORKDIR ${HOME}
# Copy directory files to image
COPY --chown=$MAMBA_USER_ID:$MAMBA_USER_GID . ${HOME}
# Settings required for conda+rstudio
ENV RSTUDIO_WHICH_R=${CONDAENV}/bin/R
ENV RETICULATE_PYTHON=${CONDAENV}/bin/python
CMD ["/init"]页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/72207945
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